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(-) Description

Title :  CRYSTAL STRUCTURE OF ICAM-5 D1-D4 ECTODOMAIN FRAGMENT, SPACE GROUP P4322
 
Authors :  R. Recacha, D. Jimenez, L. Tian, R. Barredo, C. Ghamberg, J. M. Casasnov
Date :  19 Jan 14  (Deposition) - 16 Jul 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Icam-5 Extracellular Domain, Igv, Inmunology, Icam-5, Brain, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Recacha, D. Jimenez, L. Tian, R. Barredo, C. G. Gahmberg, J. M. Casasnovas
Crystal Structures Of An Icam-5 Ectodomain Fragment Show Electrostatic-Based Homophilic Adhesions.
Acta Crystallogr. , Sect. D V. 70 1934 2014
PubMed-ID: 25004970  |  Reference-DOI: 10.1107/S1399004714009468

(-) Compounds

Molecule 1 - INTERCELLULAR ADHESION MOLECULE 5
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Fragment: D1-D4, UNP RESIDUES 32-409
    Gene: ICAM5, TLCN, TLN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ICAM-5, TELENCEPHALIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 30)

Asymmetric Unit (3, 30)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NAG26Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:23 , TRP A:51BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 23 RESIDUES 2301 TO 2302
02AC2SOFTWARESER A:19 , ASN A:43 , GLN A:55 , VAL A:57BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 43 RESIDUES 2303 TO 2304
03AC3SOFTWAREASN A:106BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 106 RESIDUES 2305 TO 2307
04AC4SOFTWAREASN A:164 , PRO A:187BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 164 RESIDUES 2308 TO 2310
05AC5SOFTWAREASP A:90 , ASN A:183BINDING SITE FOR MONO-SACCHARIDE NAG A2311 BOUND TO ASN A 183
06AC6SOFTWARETYR A:232 , ASN A:272 , ASN A:279BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 272 RESIDUES 2312 TO 2313
07AC7SOFTWAREGLN A:268 , ASN A:285BINDING SITE FOR MONO-SACCHARIDE NAG A2314 BOUND TO ASN A 285
08AC8SOFTWAREASN A:366BINDING SITE FOR MONO-SACCHARIDE NAG A2315 BOUND TO ASN A 366
09AC9SOFTWAREASN B:23 , GLN B:46 , TRP B:51BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 23 RESIDUES 2301 TO 2302
10BC1SOFTWAREASN B:43 , GLN B:55BINDING SITE FOR MONO-SACCHARIDE NAG B2303 BOUND TO ASN B 43
11BC2SOFTWAREASN B:106BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 106 RESIDUES 2304 TO 2305
12BC3SOFTWAREGLY B:162 , ASN B:164BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 164 RESIDUES 2306 TO 2307
13BC4SOFTWAREASP B:90 , VAL B:92 , ASN B:183 , SER B:184 , ALA B:186BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 183 RESIDUES 2308 TO 2310
14BC5SOFTWARETYR B:232 , ASN B:272 , ASN B:279BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 272 RESIDUES 2311 TO 2312
15BC6SOFTWAREGLN B:268 , ASN B:285BINDING SITE FOR MONO-SACCHARIDE NAG B2313 BOUND TO ASN B 285
16BC7SOFTWAREASN B:366BINDING SITE FOR MONO-SACCHARIDE NAG B2314 BOUND TO ASN B 366

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:24 -A:68
2A:28 -A:72
3A:111 -A:167
4A:218 -A:271
5A:313 -A:352
6B:24 -B:68
7B:28 -B:72
8B:111 -B:167
9B:218 -B:271
10B:313 -B:352

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Gln A:8 -Pro A:9
2Gly A:117 -Pro A:118
3Phe A:224 -Pro A:225
4Ala A:261 -Glu A:262
5Gln A:263 -Glu A:264
6Ala A:328 -Ala A:329
7Ala A:329 -Val A:330
8Gln B:8 -Pro B:9
9Gly B:117 -Pro B:118
10Phe B:224 -Pro B:225
11Ala B:261 -Glu B:262
12Pro B:301 -Ser B:302
13Ala B:329 -Val B:330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OIA)

(-) 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:374
                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee...eeeeeeee......eeeee.......eee...eeeeeee.....ee..eeeeee..eeeeee.eeeee......ee......ee...eeeeeeee....hhh.eeeeeee..eeeeeee..........eeeeeeee.......eeeeeeeeee.hhhh..eeeee...eee.eeee.....eee...eee....eeeeee...ee.....eeeeee..ee...eeeee..eeeeeeee........eeeeeeeeee..eeeeeeeeeeee..................eeee........eeee.............eeee.hhhhh...eeeeeeeee..eee....ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oia A   1 EPFWADLQPRVAFVERGGSLWLNCSTNCPRPERGGLETSLRRNGTQRGLRWLARQLVDIREPETQPVCFFRCARRTLQARGLIRTFQRPDRVELMPLPPWQPVGENFTLSCRVPGAGPRASLTLTLLRGAQELIRRSFAGEPPRARGAVLTATVLARREDHGANFSCRAELDLRPHGLGLFENSSAPRELRTFSLSPDAPRLAAPRLLEVGSERPVSCTLDGLFPASEARVYLALGDQNLSPDVTLEGDAFVATATATASAEQEGARQLVCNVTLGGENRETRENVTIYSFPAPLLTLSEPSVSEGQMVTVTCAAGAQALVTLEGVPAAVPGQPAQLQLNATENDDRRSFFCDATLDVDGETLIKNRSAELRVL 374
                                    10        20        30        40        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    


Chain B from PDB  Type:PROTEIN  Length:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee....eeeeeee......eeeee........ee...eeeeee......ee..eeeeee..eeeeee.eeeee......ee......ee...eeeeeee.....hhh.eeeeeee..eeeeeee.............eeeee.hhhhh....eeeeeee.hhhh..eeeee.......eeee.....ee....eee....eeeeeeee.ee.....eeeeee..ee...eeeee..eeeeeeee.........eeeeeeeee..eeeeeeeeeeee.....eeee.........eeeeeee.....eeee..ee.......eeeeee.hhhhh.eeeeeeeeeee..eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oia B   1 EPFWADLQPRVAFVERGGSLWLNCSTNCPRPERGGLETSLRRNGTQRGLRWLARQLVDIREPETQPVCFFRCARRTLQARGLIRTFQRPDRVELMPLPPWQPVGENFTLSCRVPGAGPRASLTLTLLRGAQELIRRSFAGEPPRARGAVLTATVLARREDHGANFSCRAELDLRPHGLGLFENSSAPRELRTFSLSPDAPRLAAPRLLEVGSERPVSCTLDGLFPASEARVYLALGDQNLSPDVTLEGDAFVATATATASAEQEGARQLVCNVTLGGENRETRENVTIYSFPAPLLTLSEPSVSEGQMVTVTCAAGAQALVTLEGVPAAVPGQPAQLQLNATENDDRRSFFCDATLDVDGETLIKNRSAELRVLY 375
                                    10        20        30        40        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
   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 4OIA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:261 - Glu A:262   [ RasMol ]  
    Ala A:328 - Ala A:329   [ RasMol ]  
    Ala A:329 - Val A:330   [ RasMol ]  
    Ala B:261 - Glu B:262   [ RasMol ]  
    Ala B:329 - Val B:330   [ RasMol ]  
    Gln A:263 - Glu A:264   [ RasMol ]  
    Gln A:8 - Pro A:9   [ RasMol ]  
    Gln B:8 - Pro B:9   [ RasMol ]  
    Gly A:117 - Pro A:118   [ RasMol ]  
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    Pro B:301 - Ser B:302   [ RasMol ]  
 
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 Related Entries

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UniProtKB/Swiss-Prot
        ICAM5_HUMAN | Q9UMF0: 3bn3 4oi9 4oib

(-) Related Entries Specified in the PDB File

4oi9 4oib