SMTL ID : 4k6t.1 (1 other biounit)

Crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor ME0385

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

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

SIA.1: 9 residues within 4Å: Chain A: Y.141, P.146, D.147, P.149, K.174 Chain B: Y.137, V.151 Ligands: 1P0.11, EDO.19 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.141, A:P.146, B:Y.137 Hydrogen bonds: A:Y.141, A:P.146, A:P.146 Water bridges: A:K.174, A:K.174, B:T.139 Salt bridges: A:K.174 SIA.10: 8 residues within 4Å: Chain B: Y.141, P.146, D.147, P.149, K.174 Chain C: Y.137, V.151 Ligands: 1P0.11 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.141, B:P.146, C:Y.137 Hydrogen bonds: B:Y.141, B:P.146 Salt bridges: B:K.174 Water bridges: C:T.139 SIA.21: 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: 1P0.11 11 PLIP interactions: 6 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: A:S.173, C:Y.141, C:P.146 Water bridges: A:T.139, A:S.171, A:S.173 Salt bridges: C:K.174

7 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: E.180 Ligands: ACT.5, ACT.15 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.180, A:E.180, ACT.15 ZN.3: 3 residues within 4Å: Chain A: H.60 Ligands: ACT.5, ACT.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.60, ACT.5, ACT.6 ZN.4: 1 residues within 4Å: Chain A: D.147 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.147 ZN.12: 3 residues within 4Å: Chain B: H.60, E.180 Ligands: ACT.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.60, B:E.180, H2O.10 ZN.13: 1 residues within 4Å: Chain B: D.87 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.87, B:D.87 ZN.14: 1 residues within 4Å: Chain B: D.147 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.147 ZN.22: 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.14, H2O.14

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

ACT.5: 6 residues within 4Å: Chain A: H.60, E.180 Ligands: ZN.2, ZN.3, ACT.6, ACT.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.60, B:K.129 ACT.6: 4 residues within 4Å: Chain A: H.60, I.61 Ligands: ZN.3, ACT.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.60 ACT.15: 6 residues within 4Å: Chain A: E.180 Chain B: K.129, K.130, Y.131 Ligands: ZN.2, ACT.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.129, B:Y.131 Salt bridges: B:K.129 ACT.16: 4 residues within 4Å: Chain B: H.60, I.61, E.180 Ligands: ZN.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.61 Hydrogen bonds: B:E.180, B:E.180 Salt bridges: B:H.60

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain A: K.111, A.112, I.113, G.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.113, A:G.114 EDO.8: 4 residues within 4Å: Chain A: K.41, G.43, S.44, E.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.41, A:E.194 EDO.17: 7 residues within 4Å: Chain B: N.24, C.25, T.26, K.31, S.89, N.90, G.92 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.26, B:S.89 Water bridges: B:D.30, B:K.93, B:K.93 EDO.18: 4 residues within 4Å: Chain B: K.111, A.112, I.113, G.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.113, B:G.114 EDO.19: 6 residues within 4Å: Chain B: P.149, A.150, V.151, W.172, S.173 Ligands: SIA.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.173, B:S.173 Water bridges: B:S.171 EDO.23: 3 residues within 4Å: Chain C: A.56, G.57, H.60 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.57 Water bridges: C:G.57, C:H.60

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 3 residues within 4Å: Chain A: K.93, A.94, Y.95 Ligand excluded by PLIP

1 x 1P0: 2,2',2''-[nitrilotris(methanediyl-1H-1,2,3-triazole-4,1-diyl)]triethanol(Non-functional Binders)

1P0.11: 3 residues within 4Å: Ligands: SIA.1, SIA.10, SIA.21 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.20: 3 residues within 4Å: Chain B: K.41, G.43, E.194 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.194, B:E.194, H2O.11 MG.24: 1 residues within 4Å: Chain C: D.147 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.147, H2O.17 MG.25: 3 residues within 4Å: Chain C: K.41, G.43, E.194 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.194, C:E.194, H2O.11

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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