SMTL ID : 4k6u.1

Crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor ME0386

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: H.60, E.180 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.60, A:E.180, H2O.4, H2O.4, H2O.5 ZN.3: 2 residues within 4Å: Chain B: H.60, E.180 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.60, B:E.180, H2O.10 ZN.6: 2 residues within 4Å: Chain C: H.60 Ligands: ACT.8 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.60, ACT.8

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

SIA.2: 9 residues within 4Å: Chain A: Y.141, P.146, D.147, P.149, K.174 Chain B: Y.137, V.151, S.173 Ligands: 1P4.5 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Y.137, B:V.151, A:Y.141, A:P.146 Hydrogen bonds: B:S.173, A:Y.141, A:P.146 Water bridges: A:K.174, A:K.174 Salt bridges: A:K.174 SIA.4: 9 residues within 4Å: Chain B: Y.141, P.146, D.147, P.149, K.174 Chain C: Y.137, V.151, S.173 Ligands: 1P4.5 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:Y.137, C:V.151, B:Y.141, B:P.146 Hydrogen bonds: C:S.173, B:Y.141, B:P.146, B:P.146 Water bridges: C:T.139 Salt bridges: B:K.174 SIA.7: 9 residues within 4Å: Chain A: Y.137, V.151, S.173 Chain C: Y.141, P.146, D.147, P.149, K.174 Ligands: 1P4.5 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:Y.137, A:V.151, C:Y.141, C:P.146 Hydrogen bonds: A:S.173, C:Y.141, C:P.146 Water bridges: A:T.139, C:K.174, C:K.174 Salt bridges: C:K.174

1 x 1P4: 3,3',3''-[nitrilotris(methanediyl-1H-1,2,3-triazole-4,1-diyl)]tripropan-1-ol(Non-functional Binders)

1P4.5: 3 residues within 4Å: Ligands: SIA.2, SIA.4, SIA.7 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 3 residues within 4Å: Chain C: H.60, I.61 Ligands: ZN.6 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.61 Salt bridges: C:H.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caraballo, R. et al., Triazole linker-based trivalent sialic acid inhibitors of adenovirus type 37 infection of human corneal epithelial cells. Org.Biomol.Chem. (2015)

Release Date

2014-10-22

Peptides

Fiber protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fiber protein

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