SMTL ID : 8qch.9 (9 other biounits)

Human Adenosine deaminase-like protein in complex with compound AT8001

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-tetramer

Ligands

4 x EIF: [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate(Non-covalent)

EIF.1: 19 residues within 4Å: Chain A: H.26, L.27, N.28, F.67, F.70, H.74, R.105, S.106, T.107, Y.121, D.148, S.180, G.181, H.208, E.211, S.263, D.293, D.294 Ligands: ZN.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.67, A:F.70 Hydrogen bonds: A:N.28, A:N.28, A:G.29, A:T.107, A:G.181, A:G.181, A:E.211, A:S.263 Water bridges: A:R.109, A:Y.121, A:S.180 Salt bridges: A:H.74, A:E.211 pi-Stacking: A:H.26, A:F.67 pi-Cation interactions: A:H.208 Halogen bonds: A:D.148 EIF.6: 18 residues within 4Å: Chain B: H.26, L.27, N.28, F.67, F.70, H.74, R.105, S.106, T.107, Y.121, D.148, S.180, G.181, H.208, E.211, D.293, D.294 Ligands: ZN.7 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.67, B:F.70 Hydrogen bonds: B:N.28, B:N.28, B:G.29, B:T.107, B:G.181, B:G.181, B:E.211 Water bridges: B:R.109 Salt bridges: B:H.74, B:E.211 pi-Stacking: B:H.26, B:F.67 Halogen bonds: B:D.148 EIF.12: 18 residues within 4Å: Chain C: H.26, L.27, N.28, F.67, F.70, H.74, R.105, S.106, T.107, Y.121, D.148, S.180, G.181, H.208, E.211, D.293, D.294 Ligands: ZN.13 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.67, C:F.70 Hydrogen bonds: C:N.28, C:N.28, C:G.29, C:T.107, C:T.107, C:Y.121, C:G.181, C:G.181 Salt bridges: C:H.74, C:E.211 pi-Stacking: C:H.26, C:F.67 pi-Cation interactions: C:H.208 Halogen bonds: C:D.148 EIF.16: 19 residues within 4Å: Chain D: H.26, L.27, N.28, G.29, F.67, F.70, H.74, R.105, S.106, T.107, D.148, R.150, S.180, G.181, H.208, E.211, D.293, D.294 Ligands: ZN.17 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:F.67, D:F.70 Hydrogen bonds: D:N.28, D:N.28, D:G.29, D:T.107, D:T.107, D:Y.121, D:G.181, D:G.181, D:S.263 Water bridges: D:R.109, D:R.150 Salt bridges: D:H.74, D:E.211 pi-Stacking: D:H.26, D:F.67 Halogen bonds: D:D.148

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.24, H.26, H.208, D.293 Ligands: EIF.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.24, A:H.26, A:H.208, A:D.293, H2O.1 ZN.7: 6 residues within 4Å: Chain B: H.24, H.26, H.208, H.232, D.293 Ligands: EIF.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.24, B:H.26, B:H.208, B:D.293, H2O.6 ZN.13: 5 residues within 4Å: Chain C: H.24, H.26, H.208, D.293 Ligands: EIF.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.24, C:H.26, C:H.208, C:D.293, H2O.9 ZN.17: 6 residues within 4Å: Chain D: H.24, H.26, H.208, H.232, D.293 Ligands: EIF.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.24, D:H.26, D:H.208, D:D.293, H2O.12

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: A.310, N.314, L.315 Chain C: A.310, N.314, L.315 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:E.311, A:N.314 Hydrogen bonds: C:N.314 SO4.4: 6 residues within 4Å: Chain A: S.318, D.322 Chain D: Y.282, A.285, L.323, E.326 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.322 SO4.5: 4 residues within 4Å: Chain A: R.142, A.333, S.334, T.337 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.334, A:S.334, A:T.337, A:T.337, A:T.337 Salt bridges: A:R.142 SO4.8: 6 residues within 4Å: Chain B: S.318, D.322 Chain C: Y.282, A.285, L.323, E.326 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.322 SO4.9: 4 residues within 4Å: Chain B: R.142, A.333, S.334, T.337 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.334, B:S.334, B:T.337, B:T.337, B:T.337 Salt bridges: B:R.142 SO4.14: 4 residues within 4Å: Chain C: R.142, A.333, S.334, T.337 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.334, C:S.334, C:T.337, C:T.337, C:T.337 Salt bridges: C:R.142 SO4.15: 6 residues within 4Å: Chain B: Y.282, A.285, L.323, E.326 Chain C: S.318, D.322 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.326, C:S.318 Water bridges: B:Y.282 SO4.18: 5 residues within 4Å: Chain A: Y.282, A.285, E.326 Chain D: S.318, D.322 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Water bridges: A:Y.282, A:S.288, A:E.326 Hydrogen bonds: D:S.318 SO4.19: 4 residues within 4Å: Chain D: R.142, A.333, S.334, T.337 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.334, D:S.334, D:S.334, D:T.337, D:T.337 Salt bridges: D:R.142

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 7 residues within 4Å: Chain B: K.349, L.353 Chain C: R.251, R.254, I.284, H.286, P.287 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.251, B:K.349, B:L.353 PEG.11: 5 residues within 4Å: Chain C: T.312, F.313, N.314 Chain D: F.313, N.314 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chazot, A. et al., The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution. Plos Biol. (2024)

Release Date

2024-07-31

Peptides

Adenosine deaminase-like protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

Adenosine deaminase-like protein

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