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(-) Description

Title :  CRYSTAL STRUCTURE OF ICAM-5 D1-D4 ECTODOMAIN FRAGMENT, SPACE GROUP P21
 
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 :  2.50
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  (4, 46)

Asymmetric/Biological Unit (4, 46)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2EDO31Ligand/Ion1,2-ETHANEDIOL
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (40, 40)

Asymmetric Unit (40, 40)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:16 , ARG A:60 , PRO A:62 , THR A:85 , PHE A:86 , GLN A:87 , ARG A:146BINDING SITE FOR RESIDUE EDO A 2316
02AC2SOFTWAREARG A:119 , PHE A:138 , VAL A:149BINDING SITE FOR RESIDUE EDO A 2317
03AC3SOFTWAREARG A:230 , VAL A:231 , VAL A:244BINDING SITE FOR RESIDUE EDO A 2318
04AC4SOFTWAREARG A:80BINDING SITE FOR RESIDUE EDO A 2319
05AC5SOFTWAREPRO A:96 , LEU A:97 , ARG A:188 , GLU A:189 , EDO A:2332BINDING SITE FOR RESIDUE EDO A 2320
06AC6SOFTWAREARG A:174 , GLY A:177 , LEU A:178 , GLY A:179BINDING SITE FOR RESIDUE EDO A 2321
07AC7SOFTWAREASP A:198 , ALA A:199BINDING SITE FOR RESIDUE EDO A 2322
08AC8SOFTWAREVAL A:11 , HOH A:2454BINDING SITE FOR RESIDUE EDO A 2323
09AC9SOFTWARESER A:19 , GLN A:55BINDING SITE FOR RESIDUE EDO A 2324
10BC1SOFTWAREGLU A:63 , HOH A:2471BINDING SITE FOR RESIDUE EDO A 2325
11BC2SOFTWAREARG A:84 , SER A:121 , HIS A:176BINDING SITE FOR RESIDUE EDO A 2326
12BC3SOFTWARETHR A:123 , GLU A:170 , ASP A:172 , ARG A:174 , HOH A:2435BINDING SITE FOR RESIDUE EDO A 2327
13BC4SOFTWAREARG A:60BINDING SITE FOR RESIDUE EDO A 2328
14BC5SOFTWAREARG A:41 , HOH A:2457BINDING SITE FOR RESIDUE EDO A 2329
15BC6SOFTWAREALA A:293 , ARG A:367BINDING SITE FOR RESIDUE EDO A 2330
16BC7SOFTWAREGLN A:46 , NAG A:2301BINDING SITE FOR RESIDUE EDO A 2331
17BC8SOFTWARELEU A:97 , PRO A:98 , PRO A:99 , GLU A:189 , ARG A:191 , EDO A:2320BINDING SITE FOR RESIDUE EDO A 2332
18BC9SOFTWAREVAL A:113 , PRO A:114 , ALA A:148 , VAL A:149BINDING SITE FOR RESIDUE EDO A 2333
19CC1SOFTWAREGLU A:182 , ASN A:183 , SER A:184BINDING SITE FOR RESIDUE EDO A 2334
20CC2SOFTWARELEU A:220 , ASP A:221BINDING SITE FOR RESIDUE EDO A 2335
21CC3SOFTWARETHR A:153BINDING SITE FOR RESIDUE EDO A 2336
22CC4SOFTWARESER A:349 , SER A:368 , ALA A:369BINDING SITE FOR RESIDUE EDO A 2337
23CC5SOFTWAREARG A:201BINDING SITE FOR RESIDUE EDO A 2338
24CC6SOFTWAREALA A:315 , GLY A:316 , PRO A:334BINDING SITE FOR RESIDUE EDO A 2339
25CC7SOFTWAREALA A:120 , GLY A:140BINDING SITE FOR RESIDUE EDO A 2340
26CC8SOFTWAREARG A:84 , HIS A:176BINDING SITE FOR RESIDUE EDO A 2341
27CC9SOFTWAREARG A:41 , ARG A:42 , ARG A:378 , EDO A:2344BINDING SITE FOR RESIDUE EDO A 2342
28DC1SOFTWAREARG A:47 , TRP A:51BINDING SITE FOR RESIDUE EDO A 2343
29DC2SOFTWARELEU A:36 , ARG A:54 , GLU A:343 , EDO A:2342BINDING SITE FOR RESIDUE EDO A 2344
30DC3SOFTWAREGLU A:264 , SER A:290BINDING SITE FOR RESIDUE EDO A 2345
31DC4SOFTWAREPRO A:242 , VAL A:244BINDING SITE FOR RESIDUE EDO A 2346
32DC5SOFTWAREASN A:23 , GLN A:46 , TRP A:51 , EDO A:2331 , HOH A:2467BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 23 RESIDUES 2301 TO 2302
33DC6SOFTWARESER A:19 , ASN A:43 , VAL A:57BINDING SITE FOR MONO-SACCHARIDE NAG A2303 BOUND TO ASN A 43
34DC7SOFTWAREGLY A:104 , ASN A:106 , THR A:153BINDING SITE FOR MONO-SACCHARIDE NAG A2304 BOUND TO ASN A 106
35DC8SOFTWAREGLY A:162 , ASN A:164BINDING SITE FOR MONO-SACCHARIDE NAG A2305 BOUND TO ASN A 164
36DC9SOFTWAREASP A:90 , ARG A:91 , VAL A:92 , ASN A:183 , HOH A:2429 , HOH A:2483BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 183 RESIDUES 2306 TO 2307
37EC1SOFTWARETYR A:232 , ASN A:272 , ASN A:279 , HOH A:2444BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 272 RESIDUES 2313 TO 2314
38EC2SOFTWAREGLN A:268 , ASN A:285 , HOH A:2418 , HOH A:2448BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 285 RESIDUES 2308 TO 2311
39EC3SOFTWAREGLN A:338 , ASN A:340 , HOH A:2433 , HOH A:2489 , HOH A:2497BINDING SITE FOR MONO-SACCHARIDE NAG A2312 BOUND TO ASN A 340
40EC4SOFTWAREASN A:366 , HOH A:2436BINDING SITE FOR MONO-SACCHARIDE NAG A2315 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  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gln A:8 -Pro A:9
2Gly A:117 -Pro A:118
3Phe A:224 -Pro A:225
4Gln A:263 -Glu A:264
5Ala A:329 -Val A:330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OI9)

(-) Exons   (0, 0)

(no "Exon" information available for 4OI9)

(-) 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:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeeee..eeeeeeeee....eeeeeee...eeeeeee...eeeeeeeee...ee..eeeeee..eeeeee.eeeee......ee......ee...eeeeeeee....hhh.eeeeeee..eeeeeee..........eeeeeeee.hhhhh...eeeeeeee.hhhh..eeeee.......eeee.....eee...eee....eeeeeee..eehhhhheeeeee...ee..eeeee..eeeeeeee.......eeeeeeeeeee..eeeeeeeeeeee.....eeee...eee...eeeeeee.....eeee..ee.......eeeeee.hhhhh.eeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oi9 A   1 EPFWADLQPRVAFVERGGSLWLNCSTNCPRPERGGLETSLRRNGTQRGLRWLARQLVDIREPETQPVCFFRCARRTLQARGLIRTFQRPDRVELMPLPPWQPVGENFTLSCRVPGAGPRASLTLTLLRGAQELIRRSFAGEPPRARGAVLTATVLARREDHGANFSCRAELDLRPHGLGLFENSSAPRELRTFSLSPDAPRLAAPRLLEVGSERPVSCTLDGLFPASEARVYLALGDQNLSPDVTLEGDAFVATATATASAEQEGARQLVCNVTLGGENRETRENVTIYSFPAPLLTLSEPSVSEGQMVTVTCAAGAQALVTLEGVPAAVPGQPAQLQLNATENDDRRSFFCDATLDVDGETLIKNRSAELRVLYAPR 378
                                    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 4OI9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OI9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OI9)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4oia 4oib