Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF NEUROLIGIN 2A FROM MOUSE
 
Authors :  X. Jin, J. Koehnke, L. Shapiro
Date :  10 Dec 07  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Neuroligin 2A, Cell Adhesion, Glycoprotein, Membrane, Phosphoprotein, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Koehnke, X. Jin, E. C. Budreck, S. Posy, P. Scheiffele, B. Honig, L. Shapiro
Crystal Structure Of The Extracellular Cholinesterase-Like Domain From Neuroligin-2.
Proc. Natl. Acad. Sci. Usa V. 105 1873 2008
PubMed-ID: 18250328  |  Reference-DOI: 10.1073/PNAS.0711701105

(-) Compounds

Molecule 1 - NEUROLIGIN-2
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System CommonHUMAN
    Expression System PlasmidPCEP4-NL2A
    Expression System StrainGNTI
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentESTERASE-LIKE DOMAIN
    GeneNLGN2, KIAA1366
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN5Ligand/IonALPHA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:41 , ARG A:52 , ASN A:98 , ASN A:574 , LYS A:576 , NAG A:702BINDING SITE FOR RESIDUE NAG A 701
02AC2SOFTWAREARG A:52 , LYS A:576 , NAG A:701 , MAN A:703BINDING SITE FOR RESIDUE NAG A 702
03AC3SOFTWARENAG A:702BINDING SITE FOR RESIDUE MAN A 703
04AC4SOFTWARETHR A:132 , TYR A:133 , ASN A:136BINDING SITE FOR RESIDUE NAG A 710
05AC5SOFTWARELYS A:230 , ASP A:356 , GLY A:357 , ASP A:358 , ASN B:98 , NAG B:802BINDING SITE FOR RESIDUE NAG B 801
06AC7SOFTWAREGLY A:225 , LYS A:230 , ASP A:356 , NAG B:801 , BMA B:803BINDING SITE FOR RESIDUE NAG B 802
07AC8SOFTWAREVAL A:355 , NAG B:802 , MAN B:804 , MAN B:806BINDING SITE FOR RESIDUE BMA B 803
08AC9SOFTWARETHR A:224 , GLY A:225 , GLN A:303 , PRO A:304 , LEU A:305 , BMA B:803BINDING SITE FOR RESIDUE MAN B 804
09AD1SOFTWAREASP A:362 , BMA B:803 , MAN B:805 , MAN B:807BINDING SITE FOR RESIDUE MAN B 806
10BC1SOFTWAREMAN B:806BINDING SITE FOR RESIDUE MAN B 805
11BC2SOFTWARETYR A:302 , ASP A:363 , MAN B:806BINDING SITE FOR RESIDUE MAN B 807
12BC3SOFTWAREASN B:136 , HOH B:812BINDING SITE FOR RESIDUE NAG B 810

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:106 -A:141
2A:317 -A:328
3A:487 -A:521
4B:106 -B:141
5B:317 -B:328
6B:487 -B:521
7C:106 -C:141
8C:317 -C:328
9C:487 -C:521
10D:106 -D:141
11D:317 -D:328
12D:487 -D:521

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln B:549 -Pro B:550

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BL8)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYLESTERASE_B_2PS00941 Carboxylesterases type-B signature 2.NLGN2_MOUSE139-149
 
 
 
  4A:139-149
B:139-149
C:139-149
D:139-149
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYLESTERASE_B_2PS00941 Carboxylesterases type-B signature 2.NLGN2_MOUSE139-149
 
 
 
  2A:139-149
-
C:139-149
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYLESTERASE_B_2PS00941 Carboxylesterases type-B signature 2.NLGN2_MOUSE139-149
 
 
 
  2-
B:139-149
-
D:139-149

(-) Exons   (0, 0)

(no "Exon" information available for 3BL8)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:556
 aligned with NLGN2_MOUSE | Q69ZK9 from UniProtKB/Swiss-Prot  Length:836

    Alignment length:570
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609
          NLGN2_MOUSE    40 RFPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPTEDGPLTKKRDEATLNPPDTDIRDSGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHLH 609
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bl8A00 A:40-609  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee...ee.........eeeeeeee......................ee......................hhhhhhhhhhhhhhhh.......eeeeeee.........--------------....eeeeeee........hhhhh.hhhhhhhhh.eeeee...hhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhh........eeeee............hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhh.......................hhhhhhhhh.....eeeeeee.....hhhhhhh......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..................hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.................hhhhh...........eeeeee....eee..hhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------CARBOXYLEST---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bl8 A  40 QKPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPTEDGPLTKK--------------DSGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHLH 609
                                    49        59        69        79        89        99       109       119       129       139       149        |-         -   |   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609
                                                                                                                                                158            173                                                                                                                                                                                                                                                                                                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:546
 aligned with NLGN2_MOUSE | Q69ZK9 from UniProtKB/Swiss-Prot  Length:836

    Alignment length:569
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599         
          NLGN2_MOUSE    40 RFPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPTEDGPLTKKRDEATLNPPDTDIRDSGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHL 608
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bl8B00 B:40-608  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.eee.........eeeeeeee......................eee.....................hhhhhhhhhhhhh..........eeeeeee.-----------------------...eeeeeee..............hhhhhhh...eeeee...hhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhh........eeeee............hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhh.......................hhhhhhhh......eeeeeee...hhhhhhhhh..........hhhhhhhhhhh...hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..................hhhhhh...............hhhhhhhhhhhhhhhhhhhhhh..................................eeeee...eee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------CARBOXYLEST--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bl8 B  40 QKPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPT-----------------------SGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHL 608
                                    49        59        69        79        89        99       109       119       129       139       149|        -         -    |  179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599         
                                                                                                                                        150                     174                                                                                                                                                                                                                                                                                                                                                                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:545
 aligned with NLGN2_MOUSE | Q69ZK9 from UniProtKB/Swiss-Prot  Length:836

    Alignment length:570
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610
          NLGN2_MOUSE    41 FPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPTEDGPLTKKRDEATLNPPDTDIRDSGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHLHN 610
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bl8C00 C:41-610  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeee.eeee.......eeeeeeeee.....hhhhh....................................hhhhhhhhhhhhhhhh.......eeeeeee.-------------------------.eeeeeee........hhhhh.hhhhhhhhh.eee.....................hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhh........eeeee............hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhh.......................hhhhhhhhh.....eeeeeee...hhhhhh.........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...................hhhhhh...............hhhhhhhhhhhhhhhhhhhhhh..................................eeee....eee...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------CARBOXYLEST----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bl8 C  41 KPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPT-------------------------KKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHLHN 610
                                    50        60        70        80        90       100       110       120       130       140       150         -         -     | 180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610
                                                                                                                                       150                       176                                                                                                                                                                                                                                                                                                                                                                                                                                                  

Chain D from PDB  Type:PROTEIN  Length:541
 aligned with NLGN2_MOUSE | Q69ZK9 from UniProtKB/Swiss-Prot  Length:836

    Alignment length:570
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610
          NLGN2_MOUSE    41 FPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPTEDGPLTKKRDEATLNPPDTDIRDSGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHLHN 610
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bl8D00 D:41-610  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....eee.eee.........eeeeeeee......................eee.....................hhhhhhhhhhhhhhh........eeeeeee.------------------------..eeeeeee........hhhhhhhhhhhhhhh.eeee....hhhhh...........hhhhhhhhhhhhhhhhhh....eeeeeeeeee.hhhhhhhhhhhh.........eeeee.....hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhh.......................hhhhhhhh......eeeeeee...hhhhh..........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..................hhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh............-----.................eeeee....ee...hhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------CARBOXYLEST----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bl8 D  41 KPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPT------------------------GKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKF-----NRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHLHN 610
                                    50        60        70        80        90       100       110       120       130       140       150         -         -    |  180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550      |  -  |    570       580       590       600       610
                                                                                                                                       150                      175                                                                                                                                                                                                                                                                                                                                                                                           557   563                                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3BL8)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BL8)

(-) Gene Ontology  (45, 45)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (NLGN2_MOUSE | Q69ZK9)
molecular function
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0042043    neurexin family protein binding    Interacting selectively and non-covalently with neurexins, synaptic cell surface proteins related to latrotoxin receptor, laminin and agrin. Neurexins act as cell recognition molecules at nerve terminals.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0097116    gephyrin clustering involved in postsynaptic density assembly    The clustering process in which gephyrin molecules are localized to distinct domains in the postsynaptic density as part of postsynaptic density assembly. Gephyrin is a component of the postsynaptic protein network of inhibitory synapses.
    GO:1904862    inhibitory synapse assembly    The aggregation, arrangement and bonding together of a set of components to form an inhibitory synapse.
    GO:0007630    jump response    The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to an external stimulus.
    GO:0035641    locomotory exploration behavior    The specific movement from place to place of an organism in response to a novel environment.
    GO:0050804    modulation of chemical synaptic transmission    Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
    GO:0050885    neuromuscular process controlling balance    Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
    GO:0007158    neuron cell-cell adhesion    The attachment of a neuron to another cell via adhesion molecules.
    GO:2000463    positive regulation of excitatory postsynaptic potential    Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    GO:0097151    positive regulation of inhibitory postsynaptic potential    Any process that activates or increases the frequency, rate or extent of inhibitory postsynaptic potential (IPSP). IPSP is a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential.
    GO:0032024    positive regulation of insulin secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.
    GO:1902474    positive regulation of protein localization to synapse    Any process that activates or increases the frequency, rate or extent of protein localization to synapse.
    GO:0051965    positive regulation of synapse assembly    Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0032230    positive regulation of synaptic transmission, GABAergic    Any process that activates, maintains or increases the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA).
    GO:0051968    positive regulation of synaptic transmission, glutamatergic    Any process that activates, maintains or increases the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
    GO:2000809    positive regulation of synaptic vesicle clustering    Any process that activates or increases the frequency, rate or extent of synaptic vesicle clustering.
    GO:0097119    postsynaptic density protein 95 clustering    The clustering process in which postsynaptic density protein 95 (PSD-95) molecules are localized to distinct domains in the cell membrane. PSD-95 is mostly located in the post synaptic density of neurons, and is involved in anchoring synaptic proteins.
    GO:0097104    postsynaptic membrane assembly    The aggregation, arrangement and bonding together of a set of components to form a postsynaptic membrane, a specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft).
    GO:0097105    presynaptic membrane assembly    The aggregation, arrangement and bonding together of a set of components to form a presynaptic membrane, including any proteins associated with the membrane, but excluding other cellular components. A presynaptic membrane is a specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction.
    GO:0035418    protein localization to synapse    Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
    GO:2000311    regulation of AMPA receptor activity    Any process that modulates the frequency, rate or extent of AMPA selective glutamate receptor activity.
    GO:0002087    regulation of respiratory gaseous exchange by neurological system process    A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0035176    social behavior    Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
    GO:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
    GO:0050808    synapse organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
    GO:0072553    terminal button organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a terminal button. A terminal button is the terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters.
    GO:0001966    thigmotaxis    The directed movement of a motile cell or organism in response to touch.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0060076    excitatory synapse    A synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0060077    inhibitory synapse    A synapse in which an action potential in the presynaptic cell reduces the probability of an action potential occurring in the postsynaptic cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0042734    presynaptic membrane    A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln B:549 - Pro B:550   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3bl8
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NLGN2_MOUSE | Q69ZK9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  NLGN2_MOUSE | Q69ZK9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3BL8)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3BL8)