SMTL ID : 7xx1.1

Crystal structure of SARS-CoV-2 N-NTD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.34, H.97, I.98 Chain B: H.11 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.34, A:H.97, B:H.11, H2O.3 ZN.2: 4 residues within 4Å: Chain B: S.31, D.34, H.97 Chain C: H.11 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.11, B:D.34, B:D.34, B:H.97, H2O.5 ZN.5: 4 residues within 4Å: Chain C: D.34, H.97, I.98 Chain D: H.11 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:D.34, C:H.97, D:H.11, H2O.8 ZN.6: 4 residues within 4Å: Chain A: H.11 Chain D: S.31, D.34, H.97 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:D.34, D:D.34, D:H.97, A:H.11, H2O.10

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 8 residues within 4Å: Chain A: W.4, N.27, I.98, N.106 Chain B: T.6, A.7, R.59, Y.61 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.27, A:N.106, B:A.7 Salt bridges: B:R.59 MES.4: 7 residues within 4Å: Chain B: W.4, N.27, N.29, I.98, N.106 Chain C: R.44, R.59 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B Water bridges: C:T.9, C:R.44, C:R.44, B:N.29 Salt bridges: C:R.44, C:R.59 Hydrogen bonds: B:N.27, B:N.106 MES.7: 8 residues within 4Å: Chain C: W.4, N.27, I.98, N.106 Chain D: T.6, A.7, R.59, Y.61 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.27, C:N.106, D:A.7 Salt bridges: D:R.59 MES.8: 6 residues within 4Å: Chain A: R.59 Chain D: W.4, N.27, N.29, I.98, N.106 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.44, D:N.106, D:N.106 Salt bridges: A:R.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luan, X. et al., Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein. Sci Bull (Beijing) (2022)

Release Date

2023-02-08

Peptides

Nucleoprotein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Nucleoprotein

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