SMTL ID : 6wkp.1

Crystal structure of RNA-binding domain of nucleocapsid phosphoprotein from SARS CoV-2, monoclinic crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: S.34, D.37, H.100 Chain D: H.14 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:H.14, A:D.37, A:H.100, H2O.1 ZN.3: 4 residues within 4Å: Chain A: H.14 Chain B: S.34, D.37, H.100 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.37, B:D.37, B:H.100, A:H.14, H2O.1 ZN.4: 4 residues within 4Å: Chain B: H.14 Chain C: S.34, D.37, H.100 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:D.37, C:H.100, B:H.14, H2O.1 ZN.6: 4 residues within 4Å: Chain C: H.14 Chain D: S.34, D.37, H.100 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:H.14, D:D.37, D:H.100, H2O.1

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

MES.2: 9 residues within 4Å: Chain A: T.9, A.10, T.12, R.62, Y.64 Chain B: W.7, N.30, N.32, N.109 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.10, B:N.30, B:N.109 MES.5: 8 residues within 4Å: Chain C: T.9, A.10, R.62, Y.64 Chain D: W.7, N.30, I.101, N.109 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.10, D:N.30 Salt bridges: C:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. Iscience (2024)

Release Date

2020-04-29

Peptides

Nucleoprotein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Nucleoprotein