SMTL ID : 6wlc.1

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-5'-Monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-hexamer

Ligands

6 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 9 residues within 4Å: Chain A: H.273, K.313, V.315, C.316, S.317, Y.366, P.367, K.368, L.369 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.273, A:S.317, A:S.317, A:S.317, A:L.369 Water bridges: A:Q.268, A:G.271, A:G.271, A:G.271, A:Y.366, A:Y.366 U5P.11: 9 residues within 4Å: Chain B: H.273, K.313, V.315, C.316, S.317, Y.366, P.367, K.368, L.369 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.366 Hydrogen bonds: B:H.273, B:S.317, B:S.317, B:S.317, B:L.369 Water bridges: B:Q.268, B:G.271, B:G.271, B:T.364 U5P.22: 9 residues within 4Å: Chain C: H.273, K.313, V.315, C.316, S.317, Y.366, P.367, K.368, L.369 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:H.273, C:S.317, C:S.317, C:S.317, C:L.369 Water bridges: C:Q.268, C:G.271, C:G.271, C:G.271, C:Y.366, C:Y.366 U5P.32: 9 residues within 4Å: Chain D: H.273, K.313, V.315, C.316, S.317, Y.366, P.367, K.368, L.369 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.366 Hydrogen bonds: D:H.273, D:S.317, D:S.317, D:S.317, D:L.369 Water bridges: D:Q.268, D:G.271, D:G.271, D:T.364 U5P.43: 9 residues within 4Å: Chain E: H.273, K.313, V.315, C.316, S.317, Y.366, P.367, K.368, L.369 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:H.273, E:S.317, E:S.317, E:S.317, E:L.369 Water bridges: E:Q.268, E:G.271, E:G.271, E:G.271, E:Y.366, E:Y.366 U5P.53: 9 residues within 4Å: Chain F: H.273, K.313, V.315, C.316, S.317, Y.366, P.367, K.368, L.369 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:Y.366 Hydrogen bonds: F:H.273, F:S.317, F:S.317, F:S.317, F:L.369 Water bridges: F:Q.268, F:G.271, F:G.271, F:T.364

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 3 residues within 4Å: Chain A: F.67, E.68, D.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.68, A:E.68 TRS.12: 7 residues within 4Å: Chain B: F.67, E.68, W.82, D.115 Chain F: E.290 Ligands: FMT.20, EDO.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.68 Water bridges: B:W.110, B:D.115 TRS.23: 3 residues within 4Å: Chain C: F.67, E.68, D.115 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.68, C:E.68 TRS.33: 7 residues within 4Å: Chain B: E.290 Chain D: F.67, E.68, W.82, D.115 Ligands: FMT.41, EDO.42 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.68 Water bridges: D:W.110, D:D.115 TRS.44: 3 residues within 4Å: Chain E: F.67, E.68, D.115 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.68, E:E.68 TRS.54: 7 residues within 4Å: Chain D: E.290 Chain F: F.67, E.68, W.82, D.115 Ligands: FMT.62, EDO.63 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.68 Water bridges: F:W.110, F:D.115

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

EDO.3: 8 residues within 4Å: Chain A: N.76, E.80, C.126, S.127, M.128 Chain D: E.27, P.47, V.48 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: N.223, L.224, Y.302 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: N.97, G.100, V.101, D.102 Chain E: D.60 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: L.335, S.336, V.337, V.338, C.357, K.358, D.359, G.360 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: E.92, V.93, W.110, Y.112, K.113, S.185, D.296 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: N.98, L.99, G.100, K.204, Y.348 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: V.172, K.173, G.174 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: S.178, V.179, E.215, T.216, F.218 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: E.215, K.343, T.345, E.350 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: E.68 Ligands: TRS.12, FMT.20 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain C: N.76, E.80, C.126, S.127, M.128 Chain F: E.27, P.47, V.48 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: N.223, L.224, Y.302 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: D.60 Chain C: N.97, G.100, V.101, D.102 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain C: L.335, S.336, V.337, V.338, C.357, K.358, D.359, G.360 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain C: E.92, V.93, W.110, Y.112, K.113, S.185, D.296 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: N.98, L.99, G.100, K.204, Y.348 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain D: V.172, K.173, G.174 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain D: S.178, V.179, E.215, T.216, F.218 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain D: E.215, K.343, T.345, E.350 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain D: E.68 Ligands: TRS.33, FMT.41 Ligand excluded by PLIP EDO.45: 8 residues within 4Å: Chain B: E.27, P.47, V.48 Chain E: N.76, E.80, C.126, S.127, M.128 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain E: N.223, L.224, Y.302 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain C: D.60 Chain E: N.97, G.100, V.101, D.102 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain E: L.335, S.336, V.337, V.338, C.357, K.358, D.359, G.360 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain E: E.92, V.93, W.110, Y.112, K.113, S.185, D.296 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain E: N.98, L.99, G.100, K.204, Y.348 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain F: V.172, K.173, G.174 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain F: S.178, V.179, E.215, T.216, F.218 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain F: E.215, K.343, T.345, E.350 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain F: E.68 Ligands: TRS.54, FMT.62 Ligand excluded by PLIP

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

ACT.4: 2 residues within 4Å: Chain A: W.356, E.363 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.356 Hydrogen bonds: A:E.363 ACT.15: 8 residues within 4Å: Chain B: L.335, S.336, V.337, V.338, C.357, K.358, D.359, G.360 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.359, B:G.360 ACT.17: 5 residues within 4Å: Chain B: E.169, K.197, Q.199, F.200, N.201 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.199 Hydrogen bonds: B:Q.199, B:N.201 Salt bridges: B:K.197 ACT.18: 7 residues within 4Å: Chain B: G.149, V.155, T.168, E.169, G.170, S.171, V.172 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.155, B:T.168 Hydrogen bonds: B:E.169, B:G.170 ACT.25: 2 residues within 4Å: Chain C: W.356, E.363 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.356 Hydrogen bonds: C:E.363 ACT.36: 8 residues within 4Å: Chain D: L.335, S.336, V.337, V.338, C.357, K.358, D.359, G.360 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.359, D:G.360 ACT.38: 5 residues within 4Å: Chain D: E.169, K.197, Q.199, F.200, N.201 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Q.199 Hydrogen bonds: D:Q.199, D:N.201 Salt bridges: D:K.197 ACT.39: 7 residues within 4Å: Chain D: G.149, V.155, T.168, E.169, G.170, S.171, V.172 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.155, D:T.168 Hydrogen bonds: D:E.169, D:G.170 ACT.46: 2 residues within 4Å: Chain E: W.356, E.363 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.356 Hydrogen bonds: E:E.363 ACT.57: 8 residues within 4Å: Chain F: L.335, S.336, V.337, V.338, C.357, K.358, D.359, G.360 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.359, F:G.360 ACT.59: 5 residues within 4Å: Chain F: E.169, K.197, Q.199, F.200, N.201 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:Q.199 Hydrogen bonds: F:Q.199, F:N.201 Salt bridges: F:K.197 ACT.60: 7 residues within 4Å: Chain F: G.149, V.155, T.168, E.169, G.170, S.171, V.172 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:V.155, F:T.168 Hydrogen bonds: F:E.169, F:G.170

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

SO4.10: 5 residues within 4Å: Chain A: E.252, G.253, Y.254, G.360, H.361 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.254 Water bridges: A:G.360 Salt bridges: A:H.361 SO4.31: 5 residues within 4Å: Chain C: E.252, G.253, Y.254, G.360, H.361 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.254 Water bridges: C:G.360 Salt bridges: C:H.361 SO4.52: 5 residues within 4Å: Chain E: E.252, G.253, Y.254, G.360, H.361 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.254 Water bridges: E:G.360 Salt bridges: E:H.361

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.19: 4 residues within 4Å: Chain B: K.70, K.113, R.114 Chain D: E.65 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.70, B:K.70 FMT.20: 3 residues within 4Å: Chain B: D.115 Ligands: TRS.12, EDO.21 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.112 FMT.40: 4 residues within 4Å: Chain D: K.70, K.113, R.114 Chain F: E.65 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.70, D:K.70 FMT.41: 3 residues within 4Å: Chain D: D.115 Ligands: TRS.33, EDO.42 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Y.112 FMT.61: 4 residues within 4Å: Chain B: E.65 Chain F: K.70, K.113, R.114 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.70, F:K.70 FMT.62: 3 residues within 4Å: Chain F: D.115 Ligands: TRS.54, EDO.63 1 PLIP interactions: 1 interactions with chain F Water bridges: F:Y.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2. Commun Biol (2021)

Release Date

2020-04-29

Peptides

Uridylate-specific endoribonuclease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Uridylate-specific endoribonuclease

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