SMTL ID : 4k6w.1

Crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor ME0408

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

3 x 18D: 3,5-dideoxy-5-(propanoylamino)-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid

18D.1: 9 residues within 4Å: Chain A: Y.141, P.146, D.147, P.149, K.174 Chain B: G.138, T.139, V.151 Ligands: 1P0.2 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.151, B:V.151, A:Y.141 Water bridges: B:T.139, A:K.174, A:K.174 Hydrogen bonds: A:Y.141, A:P.146 Salt bridges: A:K.174 18D.7: 9 residues within 4Å: Chain B: Y.141, P.146, D.147, P.149, K.174 Chain C: Y.137, T.139, V.151 Ligands: 1P0.2 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.141, C:Y.137, C:V.151, C:V.151 Hydrogen bonds: B:Y.141, B:P.146 Salt bridges: B:K.174 Water bridges: C:T.139 18D.11: 10 residues within 4Å: Chain A: Y.137, T.139, V.151, S.173 Chain C: Y.141, P.146, D.147, P.149, K.174 Ligands: 1P0.2 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Y.141, C:Y.141, A:Y.137, A:V.151, A:V.151 Hydrogen bonds: C:Y.141, C:P.146 Water bridges: C:K.174, C:K.174, A:T.139 Salt bridges: C:K.174

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

1P0.2: 3 residues within 4Å: Ligands: 18D.1, 18D.7, 18D.11 No protein-ligand interaction detected (PLIP)

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

ACT.3: 3 residues within 4Å: Chain A: I.27, K.58, Y.59 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.59 Hydrogen bonds: A:Y.59 Water bridges: A:I.27, A:T.74 Salt bridges: A:K.58 ACT.8: 6 residues within 4Å: Chain A: V.55, H.60, E.180 Chain B: K.129, Y.131 Ligands: ZN.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.60, B:K.129 Hydrogen bonds: B:Y.131 ACT.12: 3 residues within 4Å: Chain C: I.27, K.58, Y.59 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.58 ACT.13: 4 residues within 4Å: Chain C: K.124, T.160, G.161, C.162 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.160 Hydrogen bonds: C:G.161 Salt bridges: C:K.124 ACT.14: 3 residues within 4Å: Chain C: H.60, I.61 Ligands: ZN.16 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.61 Salt bridges: C:H.60

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

EDO.4: 2 residues within 4Å: Chain A: G.57, K.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.57 EDO.9: 7 residues within 4Å: Chain B: P.23, N.24, K.31, G.92, A.94, Y.95, W.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.95, B:Y.95 Water bridges: B:A.94 EDO.15: 4 residues within 4Å: Chain C: K.111, A.112, I.113, G.114 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.113, C:G.114

3 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: H.60, E.180 Ligands: ACT.8 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.60, A:E.180, H2O.8, H2O.9, ACT.8 ZN.10: 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.16, H2O.16 ZN.16: 2 residues within 4Å: Chain C: H.60 Ligands: ACT.14 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.60

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain A: D.147 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.147, H2O.8 MG.17: 1 residues within 4Å: Chain C: D.147 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.147, H2O.24, H2O.25

Links

RCSB   PDBe   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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