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(-) Description

Title :  CRYSTAL STRUCTURE OF ICAM-5 D1-D4 ECTODOMAIN FRAGMENT, SPACE GROUP R3
 
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 :  3.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Adhesion, Cell Surface, Neurons, Immunoglobulin Superfamily, Intercellular Adhesion Molecules, Icam-5, Telencephalin (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
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Fragment: D1-D4
    Gene: ICAM5, TLCN, TLN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ICAM-5, TELENCEPHALIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric/Biological Unit (3, 22)
No.NameCountTypeFull Name
1BMA5Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:23 , GLN A:46 , TRP A:51BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 23 RESIDUES 2301 TO 2303
2AC2SOFTWAREASN A:43BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 43 RESIDUES 2304 TO 2307
3AC3SOFTWAREASN A:106 , THR A:153BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 106 RESIDUES 2308 TO 2311
4AC4SOFTWAREASN A:164 , GLU A:189BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 164 RESIDUES 2312 TO 2314
5AC5SOFTWAREPRO A:89 , ASP A:90 , ASN A:183BINDING SITE FOR MONO-SACCHARIDE NAG A2315 BOUND TO ASN A 183
6AC6SOFTWARETYR A:232 , ASN A:272 , THR A:274 , GLU A:281BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 272 RESIDUES 2316 TO 2319
7AC7SOFTWAREASN A:285BINDING SITE FOR MONO-SACCHARIDE NAG A2320 BOUND TO ASN A 285
8AC8SOFTWAREASN A:340BINDING SITE FOR MONO-SACCHARIDE NAG A2321 BOUND TO ASN A 340
9AC9SOFTWAREILE A:364 , ASN A:366BINDING SITE FOR MONO-SACCHARIDE NAG A2322 BOUND TO ASN A 366

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:24 -A:68
2A:28 -A:72
3A:111 -A:167
4A:218 -A:271
5A:313 -A:352

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Glu A:1 -Pro A:2
2Pro A:2 -Phe A:3
3Gln A:8 -Pro A:9
4Gly A:117 -Pro A:118
5Phe A:224 -Pro A:225
6Glu A:264 -Gly A:265
7Ser A:299 -Glu A:300
8Ala A:329 -Val A:330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OIB)

(-) Sequences/Alignments

Asymmetric/Biological 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:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeeee..eeeeeeeee......eeeee....eeeeee...eeeeeeeee...ee..eeeeee..eeeeee.eeeee..............ee....eeeeeee....hhh.eeeeeee..eeeeeee..........eeeeeee.........eeeeeeeeee.....eeeeee...ee..ee.......eee....ee...eeeeeeee.........eeeeee..ee...eeeee..eeeeeeeee.........eeeeeeee..eeeeeeee..ee.....eeeee........eeeeeee.....eeee..ee.......eeeeee.hhhhh..eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oib A   1 EPFWADLQPRVAFVERGGSLWLNCSTNCPRPERGGLETSLRRNGTQRGLRWLARQLVDIREPETQPVCFFRCARRTLQARGLIRTFQRPDRVELMPLPPWQPVGENFTLSCRVPGAGPRASLTLTLLRGAQELIRRSFAGEPPRARGAVLTATVLARREDHGANFSCRAELDLRPHGLGLFENSSAPRELRTFSLSPDAPRLAAPRLLEVGSERPVSCTLDGLFPASEARVYLALGDQNLSPDVTLEGDAFVATATATASAEQEGARQLVCNVTLGGENRETRENVTIYSFPAPLLTLSEPSVSEGQMVTVTCAAGAQALVTLEGVPAAVPGQPAQLQLNATENDDRRSFFCDATLDVDGETLIKNRSAELR 372
                                    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
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  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 4OIB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4oi9 4oia