SMTL ID : 6x4i.1

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with 3'-uridinemonophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

6 x U3P: 3'-URIDINEMONOPHOSPHATE(Non-covalent)

U3P.1: 10 residues within 4Å: Chain A: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.271, A:E.363, A:E.363, A:Y.366 Water bridges: A:Q.268 Salt bridges: A:H.258, A:H.273, A:K.313 pi-Stacking: A:W.356, A:W.356 U3P.13: 10 residues within 4Å: Chain B: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.16 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.271, B:E.363, B:T.364 Water bridges: B:Q.268, B:K.313 Salt bridges: B:H.258, B:H.273, B:K.313 pi-Stacking: B:W.356, B:W.356 U3P.24: 10 residues within 4Å: Chain C: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.25 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.271, C:E.363, C:E.363, C:Y.366 Water bridges: C:Q.268 Salt bridges: C:H.258, C:H.273, C:K.313 pi-Stacking: C:W.356, C:W.356 U3P.36: 10 residues within 4Å: Chain D: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.39 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.271, D:E.363, D:T.364 Water bridges: D:Q.268, D:K.313 Salt bridges: D:H.258, D:H.273, D:K.313 pi-Stacking: D:W.356, D:W.356 U3P.47: 10 residues within 4Å: Chain E: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.48 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.271, E:E.363, E:E.363, E:Y.366 Water bridges: E:Q.268 Salt bridges: E:H.258, E:H.273, E:K.313 pi-Stacking: E:W.356, E:W.356 U3P.59: 10 residues within 4Å: Chain F: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.62 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.271, F:E.363, F:T.364 Water bridges: F:Q.268, F:K.313 Salt bridges: F:H.258, F:H.273, F:K.313 pi-Stacking: F:W.356, F:W.356

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

EDO.2: 7 residues within 4Å: Chain A: H.273, V.315, C.316, S.317, Y.366 Ligands: U3P.1, EDO.7 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: P.181, K.182, Q.183, F.218, Q.220 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: K.343, V.344, T.345, E.350 Ligands: EDO.11 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: A.195 Chain C: H.266, S.267 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: E.252, G.253, Y.254, L.335, G.360, H.361 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: N.301, S.317, P.367, K.368, L.369 Ligands: EDO.2 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: N.98, L.99, K.204, P.214, Y.348 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: L.66, F.67, E.68 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: E.27, P.47, V.48 Chain D: N.76, E.80, C.126, S.127, M.128 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: P.214, E.350 Ligands: EDO.4 Ligand excluded by PLIP EDO.12: 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.15: 4 residues within 4Å: Chain B: S.178, V.179, E.215, T.216 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: H.273, V.315, C.316, S.317, Y.366 Ligands: U3P.13, EDO.17 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: N.301, S.317, P.367, K.368, L.369 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: G.149, V.155, T.168, E.169, G.170, S.171 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: N.97, G.100, V.101, D.102 Chain D: D.60 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: N.98, L.99, K.204, Q.211, L.213, P.214, Y.348 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: L.66, F.67, E.68, W.82 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: F.264, R.281, Q.308, T.309 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: E.215, Y.217, V.344, T.345 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain C: H.273, V.315, C.316, S.317, Y.366 Ligands: U3P.24, EDO.30 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: P.181, K.182, Q.183, F.218, Q.220 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: K.343, V.344, T.345, E.350 Ligands: EDO.34 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain C: A.195 Chain E: H.266, S.267 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain C: E.252, G.253, Y.254, L.335, G.360, H.361 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: N.301, S.317, P.367, K.368, L.369 Ligands: EDO.25 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain C: N.98, L.99, K.204, P.214, Y.348 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain C: L.66, F.67, E.68 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain C: E.27, P.47, V.48 Chain F: N.76, E.80, C.126, S.127, M.128 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain C: P.214, E.350 Ligands: EDO.27 Ligand excluded by PLIP EDO.35: 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.38: 4 residues within 4Å: Chain D: S.178, V.179, E.215, T.216 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain D: H.273, V.315, C.316, S.317, Y.366 Ligands: U3P.36, EDO.40 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain D: N.301, S.317, P.367, K.368, L.369 Ligands: EDO.39 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain D: G.149, V.155, T.168, E.169, G.170, S.171 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain D: N.97, G.100, V.101, D.102 Chain F: D.60 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: N.98, L.99, K.204, Q.211, L.213, P.214, Y.348 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain D: L.66, F.67, E.68, W.82 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain D: F.264, R.281, Q.308, T.309 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain D: E.215, Y.217, V.344, T.345 Ligand excluded by PLIP EDO.48: 7 residues within 4Å: Chain E: H.273, V.315, C.316, S.317, Y.366 Ligands: U3P.47, EDO.53 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain E: P.181, K.182, Q.183, F.218, Q.220 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain E: K.343, V.344, T.345, E.350 Ligands: EDO.57 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain A: H.266, S.267 Chain E: A.195 Ligand excluded by PLIP EDO.52: 6 residues within 4Å: Chain E: E.252, G.253, Y.254, L.335, G.360, H.361 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain E: N.301, S.317, P.367, K.368, L.369 Ligands: EDO.48 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain E: N.98, L.99, K.204, P.214, Y.348 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain E: L.66, F.67, E.68 Ligand excluded by PLIP EDO.56: 8 residues within 4Å: Chain B: N.76, E.80, C.126, S.127, M.128 Chain E: E.27, P.47, V.48 Ligand excluded by PLIP EDO.57: 3 residues within 4Å: Chain E: P.214, E.350 Ligands: EDO.50 Ligand excluded by PLIP EDO.58: 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.61: 4 residues within 4Å: Chain F: S.178, V.179, E.215, T.216 Ligand excluded by PLIP EDO.62: 7 residues within 4Å: Chain F: H.273, V.315, C.316, S.317, Y.366 Ligands: U3P.59, EDO.63 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain F: N.301, S.317, P.367, K.368, L.369 Ligands: EDO.62 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain F: G.149, V.155, T.168, E.169, G.170, S.171 Ligand excluded by PLIP EDO.65: 5 residues within 4Å: Chain B: D.60 Chain F: N.97, G.100, V.101, D.102 Ligand excluded by PLIP EDO.66: 7 residues within 4Å: Chain F: N.98, L.99, K.204, Q.211, L.213, P.214, Y.348 Ligand excluded by PLIP EDO.67: 4 residues within 4Å: Chain F: L.66, F.67, E.68, W.82 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain F: F.264, R.281, Q.308, T.309 Ligand excluded by PLIP EDO.69: 4 residues within 4Å: Chain F: E.215, Y.217, V.344, T.345 Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.14: 2 residues within 4Å: Chain B: D.102, T.144 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.144, B:T.144 NA.37: 2 residues within 4Å: Chain D: D.102, T.144 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.144, D:T.144 NA.60: 2 residues within 4Å: Chain F: D.102, T.144 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.102, F:T.144

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

2020-06-03

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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