SMTL ID : 7kri.1

FR6-bound SARS-CoV-2 Nsp9 RNA-replicase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: H.8, M.32, S.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.33 Salt bridges: A:H.8 SO4.4: 3 residues within 4Å: Chain B: H.8, M.32, S.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.33 Salt bridges: B:H.8 SO4.7: 1 residues within 4Å: Chain C: R.59 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.59 Salt bridges: C:R.59 SO4.11: 3 residues within 4Å: Chain D: H.8, M.32, S.33 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.33 Water bridges: D:H.8 Salt bridges: D:H.8 SO4.14: 3 residues within 4Å: Chain E: H.8, M.32, S.33 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.33 Salt bridges: E:H.8 SO4.17: 1 residues within 4Å: Chain F: R.59 2 PLIP interactions: 2 interactions with chain F Water bridges: F:R.59 Salt bridges: F:R.59

12 x X0Y: 1,3-dimethyl-1H-pyrrolo[3,4-d]pyrimidine-2,4(3H,6H)-dione(Non-covalent)

X0Y.2: 10 residues within 4Å: Chain A: F.16, N.53, T.55, F.60, L.62, L.114, N.118 Chain F: Q.17, G.18 Ligands: X0Y.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.60 Hydrogen bonds: A:N.53, A:N.118 pi-Stacking: A:F.60 X0Y.3: 8 residues within 4Å: Chain A: F.16, N.53, N.115, N.118 Chain F: F.16, Q.17 Ligands: X0Y.2, X0Y.20 7 PLIP interactions: 2 interactions with chain F, 5 interactions with chain A Water bridges: F:N.118, F:N.118, A:N.53, A:N.115 Hydrogen bonds: A:N.53, A:N.118 pi-Stacking: A:F.16 X0Y.5: 11 residues within 4Å: Chain B: F.16, N.53, T.55, F.60, L.62, L.114, N.118 Chain E: Q.17, G.18, P.19 Ligands: X0Y.6 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:F.60 Hydrogen bonds: B:N.53 Water bridges: B:T.55, B:T.55, B:N.118, E:P.19 pi-Stacking: B:F.60 X0Y.6: 7 residues within 4Å: Chain B: F.16, N.53, N.115, N.118 Chain E: Q.17 Ligands: X0Y.5, X0Y.16 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:N.53, B:N.118 Water bridges: B:N.115, E:Q.17, E:N.118 pi-Stacking: B:F.16 X0Y.9: 10 residues within 4Å: Chain C: F.16, N.53, T.55, F.60, L.62, L.114, N.118 Chain D: Q.17, G.18 Ligands: X0Y.10 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.60 Hydrogen bonds: C:N.53, C:N.118 pi-Stacking: C:F.60, C:F.60 Water bridges: D:Q.17 X0Y.10: 8 residues within 4Å: Chain C: F.16, N.53, N.115, N.118 Chain D: F.16, Q.17 Ligands: X0Y.9, X0Y.13 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Water bridges: D:N.118, D:N.118, C:N.115 Hydrogen bonds: C:N.53, C:N.118 pi-Stacking: C:F.16 X0Y.12: 10 residues within 4Å: Chain C: Q.17, G.18 Chain D: F.16, N.53, T.55, F.60, L.62, L.114, N.118 Ligands: X0Y.13 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.60 Hydrogen bonds: D:N.53, D:N.118 pi-Stacking: D:F.60 X0Y.13: 8 residues within 4Å: Chain C: F.16, Q.17 Chain D: F.16, N.53, N.115, N.118 Ligands: X0Y.10, X0Y.12 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.53, D:N.118 Water bridges: D:N.53, D:N.115, C:N.118, C:N.118 pi-Stacking: D:F.16 X0Y.15: 11 residues within 4Å: Chain B: Q.17, G.18, P.19 Chain E: F.16, N.53, T.55, F.60, L.62, L.114, N.118 Ligands: X0Y.16 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:F.60 Hydrogen bonds: E:N.53 Water bridges: E:T.55, E:T.55, E:T.55, E:N.118, B:P.19 pi-Stacking: E:F.60 X0Y.16: 7 residues within 4Å: Chain B: Q.17 Chain E: F.16, N.53, N.115, N.118 Ligands: X0Y.6, X0Y.15 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:N.53, E:N.118 Water bridges: E:N.115, B:Q.17, B:N.118 pi-Stacking: E:F.16 X0Y.19: 10 residues within 4Å: Chain A: Q.17, G.18 Chain F: F.16, N.53, T.55, F.60, L.62, L.114, N.118 Ligands: X0Y.20 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:F.60 Hydrogen bonds: F:N.53, F:N.118 pi-Stacking: F:F.60, F:F.60 Water bridges: A:Q.17 X0Y.20: 8 residues within 4Å: Chain A: F.16, Q.17 Chain F: F.16, N.53, N.115, N.118 Ligands: X0Y.3, X0Y.19 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:N.53, F:N.118 Water bridges: F:N.115, A:N.118, A:N.118 pi-Stacking: F:F.16

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.8: 8 residues within 4Å: Chain B: N.116 Chain C: N.115, N.116, L.117 Chain D: N.115, N.116, L.117 Chain F: N.116 10 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: D:N.115 Hydrogen bonds: D:N.115, D:N.116, D:N.116, D:L.117, B:N.116, C:N.116, C:L.117, F:N.116 Water bridges: D:N.115 MLI.18: 8 residues within 4Å: Chain A: N.115, N.116, L.117 Chain C: N.116 Chain E: N.116 Chain F: N.115, N.116, L.117 10 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F, 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: E:N.116, F:N.116, F:L.117, A:N.115, A:N.116, A:N.116, A:L.117, C:N.116 Water bridges: F:N.115 Hydrophobic interactions: A:N.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Littler, D.R. et al., Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9. J.Biol.Chem. (2021)

Release Date

2021-07-21

Peptides

Non-structural protein 9: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Non-structural protein 9

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