Structure of PDB 3gvj Chain A Binding Site BS05

Receptor Information
>3gvj Chain A (length=670) Species: 344021 (Escherichia phage K1F) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPRGSAKGDGVTDDTAALTSALNDTPVGQKINGNGKTYKVTSLPDISRFI
NTRFVYERIPGQPLYYASEEFVQGELFKITDTPYYNAWPQDKAFVYENVI
YAPYMGSDRHGVSRLHVSWVKSGDDGQTWSTPEWLTDLHPDYPTVNYHCM
SMGVCRNRLFAMIETRTLAKNALTNCALWDRPMSRSLHLTGGITKAANQR
YATIHVPDHGLFVGDFVNFSNSAVTGVSGDMTVATVIDKDNFTVLTPNQQ
TSDLNNAGKNWHMGTSFHKSPWRKTDLGLIPSVTEVHSFATIDNNGFAMG
YHQGDVAPREVGLFYFPDAFNSPSNYVRRQIPSEYEPDASEPCIKYYDGV
LYLITRGTRGDRLGSSLHRSRDIGQTWESLRFPHNVHHTTLPFAKVGDDL
IMFGSEAAENEWEAGAPDDRYKASYPRTFYARLNVNNWNADDIEWVNITD
QIYQGGIVNSGVGVGSVVVKDNYIYYMFGGEDHFNPWTYGDNSAKDPFKS
DGHPSDLYCYKMKIGPDNRVSRDFRYGAVPNRAVPVFFDTNGVRTVPAPM
EFTGDLGLGHVTIRASTSSNIRSEVLMEGEYGFIGKSIPTDNPAGQRIIF
CGGEGTSSTTGAQITLYGANNTDSRRIVYNGDEHLFQSADVKPYNDNVTA
LGGPSNRFTTAYLGSNPIVT
Ligand information
Ligand IDSIA
InChIInChI=1S/C11H19NO9/c1-4(14)12-7-5(15)2-11(20,10(18)19)21-9(7)8(17)6(16)3-13/h5-9,13,15-17,20H,2-3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,7+,8+,9+,11+/m0/s1
InChIKeySQVRNKJHWKZAKO-YRMXFSIDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
OpenEye OEToolkits 1.5.0CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)O
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)O
ACDLabs 10.04O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
CACTVS 3.341CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
FormulaC11 H19 N O9
NameN-acetyl-alpha-neuraminic acid;
N-acetylneuraminic acid;
sialic acid;
alpha-sialic acid;
O-SIALIC ACID
ChEMBLCHEMBL1234621
DrugBankDB03721
ZINCZINC000004081651
PDB chain3gvj Chain C Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3gvj Structural basis for the recognition and cleavage of polysialic acid by the bacteriophage K1F tailspike protein EndoNF.
Resolution1.48 Å
Binding residue
(original residue number in PDB)		R837 I839 T846 S848 Q853
Binding residue
(residue number reindexed from 1)		R597 I599 T606 S608 Q613
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y325 H350 E581 R596 A647
Catalytic site (residue number reindexed from 1) Y85 H110 E341 R356 A407
Enzyme Commision number 3.2.1.129: endo-alpha-sialidase.
Gene Ontology
Molecular Function
GO:0016996 endo-alpha-(2,8)-sialidase activity

View graph for
Molecular Function
External links
PDB RCSB:3gvj, PDBe:3gvj, PDBj:3gvj
PDBsum3gvj
PubMed20096705
UniProtQ04830|FIBER_BPK1F Tail spike protein

[Back to BioLiP]