SMTL ID : 6w01.1

The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: L.66, F.67, E.68, W.82 Ligand excluded by PLIP EDO.2: 8 residues within 4Å: Chain A: E.27, P.47, V.48 Chain F: N.76, E.80, C.126, S.127, M.128 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: I.192, G.193, E.194 Ligand excluded by PLIP EDO.4: 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.7: 4 residues within 4Å: Chain A: N.97, G.100, V.101, D.102 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: E.252, G.253, Y.254, L.335, G.360, H.361 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: R.222, N.223, L.224, L.275, Y.302 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: Y.249, V.327, K.331 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain A: E.328 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: P.181, K.182, Q.183, Q.220, R.230 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: V.179, E.215, T.216, F.218 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: F.67, W.82, W.110, D.115 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain B: E.27, P.47, V.48 Chain C: N.76, E.80, C.126, S.127, M.128 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: N.98, S.297, T.298, V.299, I.351 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: N.97, G.100, V.101, D.102 Chain F: D.60 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Chain B: S.171 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: E.169, V.179, K.197, Q.199, F.200, N.201 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: P.181, K.182, Q.183, Q.220, R.230 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: S.171, V.172, K.173, G.174, L.175 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: S.178, V.179, E.215, T.216, F.218 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: E.215, Y.217, V.344, T.345 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: T.168, E.169, G.170, S.171 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain C: L.66, F.67, E.68, W.82 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain B: N.76, E.80, C.126, S.127, M.128 Chain C: E.27, P.47, V.48 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain C: I.192, G.193, E.194 Ligand excluded by PLIP EDO.31: 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.34: 4 residues within 4Å: Chain C: N.97, G.100, V.101, D.102 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain C: E.252, G.253, Y.254, L.335, G.360, H.361 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain C: R.222, N.223, L.224, L.275, Y.302 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain C: Y.249, V.327, K.331 Ligand excluded by PLIP EDO.38: 1 residues within 4Å: Chain C: E.328 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain C: P.181, K.182, Q.183, Q.220, R.230 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain C: V.179, E.215, T.216, F.218 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain D: F.67, W.82, W.110, D.115 Ligand excluded by PLIP EDO.43: 8 residues within 4Å: Chain D: E.27, P.47, V.48 Chain E: N.76, E.80, C.126, S.127, M.128 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain D: N.98, S.297, T.298, V.299, I.351 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain B: D.60 Chain D: N.97, G.100, V.101, D.102 Ligand excluded by PLIP EDO.46: 1 residues within 4Å: Chain D: S.171 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain D: E.169, V.179, K.197, Q.199, F.200, N.201 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain D: P.181, K.182, Q.183, Q.220, R.230 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain D: S.171, V.172, K.173, G.174, L.175 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain D: S.178, V.179, E.215, T.216, F.218 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain D: E.215, Y.217, V.344, T.345 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain D: T.168, E.169, G.170, S.171 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain E: L.66, F.67, E.68, W.82 Ligand excluded by PLIP EDO.56: 8 residues within 4Å: Chain D: 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: I.192, G.193, E.194 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 E: N.97, G.100, V.101, D.102 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain E: E.252, G.253, Y.254, L.335, G.360, H.361 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain E: R.222, N.223, L.224, L.275, Y.302 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain E: Y.249, V.327, K.331 Ligand excluded by PLIP EDO.65: 1 residues within 4Å: Chain E: E.328 Ligand excluded by PLIP EDO.67: 5 residues within 4Å: Chain E: P.181, K.182, Q.183, Q.220, R.230 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain E: V.179, E.215, T.216, F.218 Ligand excluded by PLIP EDO.69: 4 residues within 4Å: Chain F: F.67, W.82, W.110, D.115 Ligand excluded by PLIP EDO.70: 8 residues within 4Å: Chain A: N.76, E.80, C.126, S.127, M.128 Chain F: E.27, P.47, V.48 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain F: N.98, S.297, T.298, V.299, I.351 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain D: D.60 Chain F: N.97, G.100, V.101, D.102 Ligand excluded by PLIP EDO.73: 1 residues within 4Å: Chain F: S.171 Ligand excluded by PLIP EDO.74: 6 residues within 4Å: Chain F: E.169, V.179, K.197, Q.199, F.200, N.201 Ligand excluded by PLIP EDO.75: 5 residues within 4Å: Chain F: P.181, K.182, Q.183, Q.220, R.230 Ligand excluded by PLIP EDO.77: 5 residues within 4Å: Chain F: S.171, V.172, K.173, G.174, L.175 Ligand excluded by PLIP EDO.78: 5 residues within 4Å: Chain F: S.178, V.179, E.215, T.216, F.218 Ligand excluded by PLIP EDO.80: 4 residues within 4Å: Chain F: E.215, Y.217, V.344, T.345 Ligand excluded by PLIP EDO.81: 4 residues within 4Å: Chain F: T.168, E.169, G.170, S.171 Ligand excluded by PLIP

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

PEG.5: 8 residues within 4Å: Chain A: H.273, N.301, V.315, C.316, S.317, Y.366, L.369 Ligands: CIT.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.273, A:N.301, A:S.317, A:L.369 PEG.6: 6 residues within 4Å: Chain A: N.98, L.99, G.100, K.204, P.214, Y.348 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.204 PEG.25: 5 residues within 4Å: Chain B: N.98, L.99, G.100, K.204, Y.348 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.204, B:Y.348 PEG.32: 8 residues within 4Å: Chain C: H.273, N.301, V.315, C.316, S.317, Y.366, L.369 Ligands: CIT.39 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.273, C:N.301, C:S.317, C:L.369 PEG.33: 6 residues within 4Å: Chain C: N.98, L.99, G.100, K.204, P.214, Y.348 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.204 PEG.52: 5 residues within 4Å: Chain D: N.98, L.99, G.100, K.204, Y.348 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.204, D:Y.348 PEG.59: 8 residues within 4Å: Chain E: H.273, N.301, V.315, C.316, S.317, Y.366, L.369 Ligands: CIT.66 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:H.273, E:N.301, E:S.317, E:L.369 PEG.60: 6 residues within 4Å: Chain E: N.98, L.99, G.100, K.204, P.214, Y.348 1 PLIP interactions: 1 interactions with chain E Water bridges: E:K.204 PEG.79: 5 residues within 4Å: Chain F: N.98, L.99, G.100, K.204, Y.348 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.204, F:Y.348

6 x CIT: CITRIC ACID(Non-functional Binders)

CIT.12: 10 residues within 4Å: Chain A: H.258, Q.268, L.269, G.270, G.271, H.273, K.313, T.364, Y.366 Ligands: PEG.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.366 Hydrogen bonds: A:Q.268, A:G.271, A:T.364 Salt bridges: A:H.258, A:H.258, A:H.273, A:K.313, A:K.313 CIT.22: 9 residues within 4Å: Chain B: H.258, Q.268, L.269, G.270, G.271, H.273, K.313, T.364, Y.366 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.366 Hydrogen bonds: B:Q.268, B:G.271 Water bridges: B:V.315 Salt bridges: B:H.258, B:H.258, B:H.273, B:K.313, B:K.313 CIT.39: 10 residues within 4Å: Chain C: H.258, Q.268, L.269, G.270, G.271, H.273, K.313, T.364, Y.366 Ligands: PEG.32 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.366 Hydrogen bonds: C:Q.268, C:G.271, C:T.364 Salt bridges: C:H.258, C:H.258, C:H.273, C:K.313, C:K.313 CIT.49: 9 residues within 4Å: Chain D: H.258, Q.268, L.269, G.270, G.271, H.273, K.313, T.364, Y.366 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.366 Hydrogen bonds: D:Q.268, D:G.271 Water bridges: D:V.315 Salt bridges: D:H.258, D:H.258, D:H.273, D:K.313, D:K.313 CIT.66: 10 residues within 4Å: Chain E: H.258, Q.268, L.269, G.270, G.271, H.273, K.313, T.364, Y.366 Ligands: PEG.59 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:Y.366 Hydrogen bonds: E:Q.268, E:G.271, E:T.364 Salt bridges: E:H.258, E:H.258, E:H.273, E:K.313, E:K.313 CIT.76: 9 residues within 4Å: Chain F: H.258, Q.268, L.269, G.270, G.271, H.273, K.313, T.364, Y.366 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:Y.366 Hydrogen bonds: F:Q.268, F:G.271 Water bridges: F:V.315 Salt bridges: F:H.258, F:H.258, F:H.273, F:K.313, F:K.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2. Protein Sci. (2020)

Release Date

2020-03-11

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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