SMTL ID : 6vww.1

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

27 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: L.66, F.67, E.68, W.82 Chain C: E.290 Ligand excluded by PLIP GOL.2: 5 residues within 4Å: Chain A: G.149, R.150, T.168, E.169, G.170 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: G.100, D.102, P.142, T.144 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: E.92, K.113, T.190, S.221, N.223 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain B: N.98, S.297, T.298, V.299 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain B: E.92, K.113, T.190, S.221, R.222, N.223 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain B: G.100, D.102, P.142, T.144 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain B: L.66, F.67, E.68, W.82 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: E.215, V.344, T.345, E.350 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain C: L.66, F.67, E.68, W.82 Chain E: E.290 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain C: G.149, R.150, T.168, E.169, G.170 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain C: G.100, D.102, P.142, T.144 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain C: E.92, K.113, T.190, S.221, N.223 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain D: N.98, S.297, T.298, V.299 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain D: E.92, K.113, T.190, S.221, R.222, N.223 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain D: G.100, D.102, P.142, T.144 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain D: L.66, F.67, E.68, W.82 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain D: E.215, V.344, T.345, E.350 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain A: E.290 Chain E: L.66, F.67, E.68, W.82 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain E: G.149, R.150, T.168, E.169, G.170 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain E: G.100, D.102, P.142, T.144 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain E: E.92, K.113, T.190, S.221, N.223 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain F: N.98, S.297, T.298, V.299 Ligand excluded by PLIP GOL.36: 6 residues within 4Å: Chain F: E.92, K.113, T.190, S.221, R.222, N.223 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain F: G.100, D.102, P.142, T.144 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain F: L.66, F.67, E.68, W.82 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain F: E.215, V.344, T.345, E.350 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: R.281, S.285, P.286, D.306, A.307, Q.308 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.285, A:P.286, A:D.306 MG.17: 6 residues within 4Å: Chain C: R.281, S.285, P.286, D.306, A.307, Q.308 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.285, C:P.286, C:D.306 MG.31: 6 residues within 4Å: Chain E: R.281, S.285, P.286, D.306, A.307, Q.308 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:S.285, E:P.286, E:D.306

9 x ACY: ACETIC ACID(Non-functional Binders)

ACY.6: 3 residues within 4Å: Chain A: N.223, L.224, Y.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.224, A:Y.302 ACY.13: 6 residues within 4Å: Chain B: E.169, V.179, K.197, Q.199, F.200, N.201 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.169 Salt bridges: B:K.197 ACY.14: 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 ACY.20: 3 residues within 4Å: Chain C: N.223, L.224, Y.302 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.224, C:Y.302 ACY.27: 6 residues within 4Å: Chain D: E.169, V.179, K.197, Q.199, F.200, N.201 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.169 Salt bridges: D:K.197 ACY.28: 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 ACY.34: 3 residues within 4Å: Chain E: N.223, L.224, Y.302 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.224, E:Y.302 ACY.41: 6 residues within 4Å: Chain F: E.169, V.179, K.197, Q.199, F.200, N.201 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.169 Salt bridges: F:K.197 ACY.42: 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

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain B: V.172, K.173, G.174 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: V.172, K.173, G.174 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain F: V.172, K.173, G.174 Ligand excluded by PLIP

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

2020-03-04

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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