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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NECTIN-LIKE 5 FULL ECTODOMAIN (D1-D3)
 
Authors :  O. J. Harrison, X. Jin, J. Brasch, L. Shapiro
Date :  25 Jun 12  (Deposition) - 22 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Immunoglobulin-Like Domain, Ig Domain, Viral Entry Receptor, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. J. Harrison, J. Vendome, J. Brasch, X. Jin, S. Hong, P. S. Katsamba, G. Ahlsen, R. B. Troyanovsky, S. M. Troyanovsky, B. Honig, L. Shapiro
Nectin Ectodomain Structures Reveal A Canonical Adhesive Interface.
Nat. Struct. Mol. Biol. V. 19 906 2012
PubMed-ID: 22902367  |  Reference-DOI: 10.1038/NSMB.2366

(-) Compounds

Molecule 1 - POLIOVIRUS RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Common: HUMAN
    Expression System Plasmid: PCEP4
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: ECTODOMAIN (D1-D3, UNP RESIDUES 28-334)
    Gene: PVR, PVS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NECTIN-LIKE PROTEIN 5, NECL-5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:50 , VAL A:95 , ALA A:96 , ASN A:105 , NAG A:402BINDING SITE FOR RESIDUE NAG A 401
02AC2SOFTWARENAG A:401 , BMA A:403BINDING SITE FOR RESIDUE NAG A 402
03AC3SOFTWARENAG A:402BINDING SITE FOR RESIDUE BMA A 403
04AC4SOFTWAREGLY A:119 , ASN A:120 , TRP A:138 , NAG A:405 , FUC A:406BINDING SITE FOR RESIDUE NAG A 404
05AC5SOFTWARETRP A:138 , NAG A:404 , BMA A:407BINDING SITE FOR RESIDUE NAG A 405
06AC6SOFTWAREASN A:120 , NAG A:404BINDING SITE FOR RESIDUE FUC A 406
07AC7SOFTWARENAG A:405 , MAN A:408BINDING SITE FOR RESIDUE BMA A 407
08AC8SOFTWAREBMA A:407BINDING SITE FOR RESIDUE MAN A 408
09AC9SOFTWAREASN A:188 , NAG A:410BINDING SITE FOR RESIDUE NAG A 409
10BC1SOFTWARENAG A:409BINDING SITE FOR RESIDUE NAG A 410
11BC2SOFTWAREASN A:218 , NAG A:412 , NAG A:413BINDING SITE FOR RESIDUE NAG A 411
12BC3SOFTWARENAG A:411BINDING SITE FOR RESIDUE NAG A 412
13BC4SOFTWAREGLY A:216 , ASN A:218 , ASN A:237 , NAG A:411 , NAG A:414BINDING SITE FOR RESIDUE NAG A 413
14BC5SOFTWARENAG A:413 , BMA A:415BINDING SITE FOR RESIDUE NAG A 414
15BC6SOFTWARENAG A:414BINDING SITE FOR RESIDUE BMA A 415
16BC7SOFTWAREPRO A:305 , ASN A:307 , FUC A:417 , NAG A:418BINDING SITE FOR RESIDUE NAG A 416
17BC8SOFTWARENAG A:416 , NAG A:418BINDING SITE FOR RESIDUE FUC A 417
18BC9SOFTWARENAG A:416 , FUC A:417 , BMA A:419BINDING SITE FOR RESIDUE NAG A 418
19CC1SOFTWARENAG A:418BINDING SITE FOR RESIDUE BMA A 419
20CC2SOFTWAREASN A:313 , THR A:315 , GLN A:322BINDING SITE FOR RESIDUE NAG A 420

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:49 -A:123
2A:166 -A:221
3A:266 -A:312

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:38 -Gly A:39
2Phe A:128 -Pro A:129
3Arg A:172 -Pro A:173
4Asn A:271 -Pro A:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FQP)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...ee.......eee..eee..........eeeeee.......eeee...eeee.....eee.............eee...hhhhheeeeeeee.....eeeeeeee......eeeeee.........eeeeeeeeeee....eeeeee....eeeeeeee......eeeeeeeee..hhhhh..eeeeeee.......eeeeee....eeeeeeee.....ee.....eeeeeeeeee....eeeeee........eeee..eeee.......eeeeeeeee....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fqp A  28 DVVVQAPTQVPGFLGDSVTLPCYLQVPNMEVTHVSQLTWARHGESGSMAVFHQTQGPSYSESKRLEFVAARLGAELRNASLRMFGLRVEDEGNYTCLFVTFPQGSRSVDIWLRVLAKPQNTAEVQKVQLTGEPVPMARCVSTGGRPPAQITWHSDLGGMPNTSQVPGFLSGTVTVTSLWILVPSSQVDGKNVTCKVEHESFEKPQLLTVNLTVYYPPEVSISGYDNNWYLGQNEATLTCDARSNPEPTGYNWSTTMGPLPPFAVAQGAQLLIRPVDKPINTTLICNVTNALGARQAELTVQVKEGP 333
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327
   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 4FQP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Pro A:38 - Gly A:39   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PVR_HUMAN | P15151: 1dgi 1nn8 3epc 3epd 3epf 3j8f 3j9f 3udw 3uro

(-) Related Entries Specified in the PDB File

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