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(-) Description

Title :  STRUCTURE OF GEPHYRIN E DOMAIN WITH GLYCINE-BETA RECEPTOR PEPTIDE
 
Authors :  V. B. Kasaragod, H. M. Maric, H. Schindelin
Date :  17 Apr 14  (Deposition) - 27 Aug 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Scaffolding Protein, Neurotransmitter Receptor Anchoring Protein, Molybdenum Cofactor Biosynthesis, Structural Protein-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. M. Maric, V. B. Kasaragod, H. Schindelin
Modulation Of Gephyrin-Glycine Receptor Affinity By Multivalency.
Acs Chem. Biol. V. 9 2554 2014
PubMed-ID: 25137389  |  Reference-DOI: 10.1021/CB500303A

(-) Compounds

Molecule 1 - GEPHYRIN
    Chains: A
    EC Number: 2.7.7.75, 2.10.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: E-DOMAIN (UNP RESIDUES 350-768)
    Gene: GPHN, GPH
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: PUTATIVE GLYCINE RECEPTOR-TUBULIN LINKER PROTEIN
 
Molecule 2 - GLYCINE RECEPTOR SUBUNIT BETA
    Chains: C
    Engineered: YES
    Fragment: UNP RESIDUES 419-433
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLYCINE RECEPTOR 58 KDA SUBUNIT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (2x): AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL8Ligand/IonGLYCEROL
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL16Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:664 , GLN A:718 , HIS A:723binding site for residue GOL A 801
2AC2SOFTWAREALA A:356 , ASN A:496 , HOH A:1070binding site for residue GOL A 802
3AC3SOFTWAREVAL A:500 , ARG A:564 , ALA A:565 , ASP A:566 , LYS A:619 , ACT A:809 , HOH A:980binding site for residue GOL A 803
4AC4SOFTWARETHR A:342 , GLU A:343 , GLU A:494 , SER A:563binding site for residue GOL A 804
5AC5SOFTWAREVAL A:359 , TYR A:360 , HOH A:998binding site for residue GOL A 805
6AC6SOFTWAREGLY A:474 , ILE A:649 , LEU A:650 , ASP A:651 , ARG A:704 , HOH A:903 , HOH A:940 , HOH A:941binding site for residue GOL A 806
7AC7SOFTWAREGLU A:536 , SER A:705 , ALA A:706 , ILE A:733 , GLY A:734 , GOL A:808 , HOH A:902 , HOH A:914binding site for residue GOL A 807
8AC8SOFTWAREGLY A:478 , PRO A:479 , SER A:480 , GLU A:481 , ARG A:675 , SER A:705 , ALA A:706 , GOL A:807 , HOH A:911 , HOH A:926binding site for residue GOL A 808
9AC9SOFTWAREGLU A:343 , ARG A:353 , LYS A:497 , PHE A:498 , GOL A:803binding site for residue ACT A 809

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PD1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:365 -Pro A:366
2Lys A:602 -Pro A:603

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PD1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PD1)

(-) Exons   (0, 0)

(no "Exon" information available for 4PD1)

(-) 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:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh....eeeee.hhh........ee.........ee...eeeehhhhh.eeeeeeeee.............eeeee...........eeee...eeeeee......eeeeee.........ee..........eee......hhhhhhhhhhhh..eeeee....eeeeee...ee..........ee.hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeee...........eeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhh........eeeeee...ee.....eeeeeeee........eeee...hhhhh...eeeee........ee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pd1 A 321 FPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTSRLMSMRSANGLLMLPPKTEQYVELHKGEVVDVMVIGL 736
                                   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  ||   586       596       606       616       626       636       646       656       666       676       686     ||701       711       721       731  ||
                                                                                                                                                                                                                                                                                      573|                                                                                                             692|                                 734|
                                                                                                                                                                                                                                                                                       580                                                                                                              698                                  736


Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4pd1 C 397 DFSIVGSLPR 406
                                   406
   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 4PD1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PD1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PD1)

(-) Gene Ontology  (63, 73)

Asymmetric Unit(hide GO term definitions)

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    Leu A:365 - Pro A:366   [ RasMol ]  
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 Related Entries

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        GEPH_RAT | Q03555: 1ihc 1t3e 2fts 2fu3 4pd0 4tk1 4tk2 4tk3 4tk4 4u90 4u91 5erq 5err 5ers 5ert 5eru 5erv
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(-) Related Entries Specified in the PDB File

4pd0