SMTL ID : 3qnd.3 (2 other biounits)

crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: E.110 Chain D: D.87 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.87 ZN.2: 2 residues within 4Å: Chain A: H.60, E.180 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.60, A:E.180, H2O.1, H2O.1 ZN.4: 2 residues within 4Å: Chain B: H.60, E.180 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.60, B:E.180, H2O.4, H2O.4 ZN.6: 2 residues within 4Å: Chain C: H.60, E.180 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.60, C:E.180, H2O.1, H2O.5 ZN.8: 2 residues within 4Å: Chain D: H.60, E.180 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.60, D:E.180, H2O.7 ZN.10: 2 residues within 4Å: Chain E: H.60, E.180 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.60, E:E.180, H2O.9, H2O.12 ZN.12: 2 residues within 4Å: Chain F: H.60, E.180 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.60, F:E.180

6 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.3: 8 residues within 4Å: Chain A: Y.141, P.146, D.147, P.149, K.174 Chain B: Y.137, V.151, S.173 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.141, A:P.146, B:Y.137, B:V.151 Hydrogen bonds: A:P.146, B:S.173 Water bridges: A:Y.141 Salt bridges: A:K.174 SIA.5: 8 residues within 4Å: Chain B: Y.141, P.146, D.147, P.149, K.174 Chain C: Y.137, V.151, S.173 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Y.137, C:V.151, B:Y.141 Hydrogen bonds: C:S.173, B:Y.141, B:P.146 Water bridges: C:T.139 Salt bridges: B:K.174 SIA.7: 8 residues within 4Å: Chain A: Y.137, V.151, S.173 Chain C: Y.141, P.146, D.147, P.149, K.174 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:Y.137, A:V.151, C:Y.141, C:P.146 Hydrogen bonds: C:P.146 Water bridges: C:Y.141 Salt bridges: C:K.174 SIA.9: 7 residues within 4Å: Chain D: Y.141, P.146, D.147, P.149, K.174 Chain E: Y.137, V.151 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:Y.141, D:P.146, E:Y.137, E:V.151 Hydrogen bonds: D:Y.141, D:P.146 Salt bridges: D:K.174 Water bridges: E:T.139 SIA.11: 7 residues within 4Å: Chain E: Y.141, P.146, D.147, P.149, K.174 Chain F: Y.137, V.151 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:Y.141, F:Y.137, F:V.151 Hydrogen bonds: E:P.146, E:P.146 Salt bridges: E:K.174 SIA.13: 8 residues within 4Å: Chain D: Y.137, V.151, S.173 Chain F: Y.141, P.146, D.147, P.149, K.174 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain F Hydrophobic interactions: D:Y.137, D:V.151, F:Y.141, F:P.146 Water bridges: D:T.139, D:S.171 Hydrogen bonds: F:Y.141, F:P.146 Salt bridges: F:K.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spjut, S. et al., A potent trivalent sialic Acid inhibitor of adenovirus type 37 infection of human corneal cells. Angew.Chem.Int.Ed.Engl. (2011)

Release Date

2011-06-15

Peptides

Fiber protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
A

E
B

F
C

Fiber protein

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