SMTL ID : 4k6t.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.60, E.180 Ligands: ACT.16 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.60, A:E.180, H2O.4, H2O.9 ZN.2: 1 residues within 4Å: Chain A: D.147 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.147 ZN.13: 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.14: 1 residues within 4Å: Chain B: D.147 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.147, H2O.10 ZN.22: 1 residues within 4Å: Chain C: H.60 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.60 ZN.23: 2 residues within 4Å: Chain A: K.129 Chain C: E.180 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.180, C:E.180 ZN.24: 1 residues within 4Å: Chain C: D.147 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.147

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

SIA.3: 7 residues within 4Å: Chain A: Y.141, P.146, D.147, P.149, K.174 Chain B: Y.137, V.151 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.137, B:V.151, A:Y.141, A:P.146 Hydrogen bonds: A:P.146, A:P.146 Salt bridges: A:K.174 SIA.15: 8 residues within 4Å: Chain B: Y.141, P.146, D.147, P.149, K.174 Chain C: Y.137, V.151, S.173 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Y.137, C:V.151, B:Y.141, B:P.146 Hydrogen bonds: C:S.173, B:P.146 Salt bridges: B:K.174 SIA.25: 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: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Y.137, A:V.151, C:Y.141, C:P.146 Hydrogen bonds: A:S.173, C:P.146 Salt bridges: C:K.174

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

ACT.4: 2 residues within 4Å: Chain A: E.177 Ligands: ACT.6 No protein-ligand interaction detected (PLIP) ACT.5: 3 residues within 4Å: Chain A: K.65, T.175 Ligands: ACT.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.65 ACT.6: 4 residues within 4Å: Chain A: K.65, E.177 Ligands: ACT.4, ACT.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.65 ACT.16: 6 residues within 4Å: Chain A: V.55, H.60, E.180 Chain B: K.129, Y.131 Ligands: ZN.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:H.60 Salt bridges: A:H.60, B:K.129 ACT.26: 7 residues within 4Å: Chain B: D.11, R.99 Chain C: K.41, G.43, S.44, E.194 Ligands: CA.29 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:K.41, B:R.99

7 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.130, I.135, K.153, T.155 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.130, A:K.153, A:K.153 Water bridges: A:Q.158, A:T.167 EDO.9: 3 residues within 4Å: Chain A: T.26, S.89, N.90 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain A: E.163 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.163 EDO.17: 3 residues within 4Å: Chain B: A.56, G.57, H.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.57 Water bridges: B:I.61 EDO.18: 5 residues within 4Å: Chain B: K.111, A.112, I.113, G.114, E.194 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.113, B:G.114, B:E.194, B:E.194 EDO.19: 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:K.31, B:Y.95, B:Y.95

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain A: T.160, G.161, C.162 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.161, A:C.162 GOL.27: 5 residues within 4Å: Chain C: K.145, Q.148, N.178, V.179, E.180 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.148, C:E.180 Water bridges: C:Q.148, C:E.180 GOL.28: 7 residues within 4Å: Chain C: K.41, K.111, A.112, I.113, G.114, F.115, E.194 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.112, C:I.113, C:G.114, C:E.194

3 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain A: K.41, G.43, E.194 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.194, A:E.194, H2O.5, H2O.5 MG.20: 2 residues within 4Å: Chain B: D.30, K.31 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.30 MG.21: 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.10

1 x CA: CALCIUM ION(Non-covalent)

CA.29: 4 residues within 4Å: Chain C: K.41, G.43, E.194 Ligands: ACT.26 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:E.194, C:E.194, ACT.26

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
E

B
F

C
G

Fiber protein

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