SMTL ID : 6vyo.1

Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

MES.1: 6 residues within 4Å: Chain A: W.7, N.30, N.32, I.101, N.109 Chain D: R.62 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:N.30, A:N.32, A:N.109, D:R.47 Water bridges: D:R.47 Salt bridges: D:R.62 MES.3: 8 residues within 4Å: Chain A: T.9, A.10, R.62 Chain B: W.7, N.30, N.32, N.109 Ligands: CL.2 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.10, B:N.30, B:N.109 Salt bridges: A:R.62 Water bridges: B:N.108 MES.8: 8 residues within 4Å: Chain B: R.47, R.62 Chain C: W.7, N.30, N.32, I.101, N.109, I.112 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:N.30, C:N.32, C:N.109 Water bridges: B:T.12, B:R.47, B:R.62, B:R.62 Salt bridges: B:R.47, B:R.62 MES.13: 7 residues within 4Å: Chain C: T.9, A.10, R.62 Chain D: W.7, N.30, N.109 Ligands: CL.11 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:N.30, D:N.109, D:N.109, C:A.10 Water bridges: D:N.32, D:N.108, D:N.108, C:R.62, C:R.62, C:R.62, C:R.62 Salt bridges: C:R.62

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

CL.2: 8 residues within 4Å: Chain A: H.14 Chain B: N.32, S.33, D.37, H.100, I.101 Ligands: MES.3, ZN.6 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: S.34, D.37, H.100 Chain D: H.14 Ligands: ZN.4 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: H.14 Chain C: S.34, D.37, H.100 Ligands: ZN.9 Ligand excluded by PLIP CL.11: 9 residues within 4Å: Chain C: T.12, H.14 Chain D: N.32, S.33, D.37, H.100, I.101 Ligands: MES.13, ZN.14 Ligand excluded by PLIP

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: S.34, D.37, H.100 Chain D: H.14 Ligands: CL.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Metal complexes: A:D.37, A:D.37, A:H.100, D:H.14 ZN.6: 5 residues within 4Å: Chain A: H.14 Chain B: D.37, H.100, I.101 Ligands: CL.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.37, B:H.100, A:H.14 ZN.9: 5 residues within 4Å: Chain B: H.14 Chain C: S.34, D.37, H.100 Ligands: CL.10 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.14, C:D.37, C:D.37, C:H.100 ZN.14: 5 residues within 4Å: Chain C: H.14 Chain D: D.37, H.100, I.101 Ligands: CL.11 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:D.37, D:H.100, C:H.14

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain B: R.23, Y.78, W.87 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.23 Water bridges: B:F.21, B:P.22, B:W.87, B:W.87 GOL.12: 6 residues within 4Å: Chain C: N.30, T.31, S.33, S.34, P.35, Q.38 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.34 Water bridges: C:N.30, C:T.31, C:Q.38 GOL.15: 3 residues within 4Å: Chain D: R.23, Y.78, W.87 6 PLIP interactions: 6 interactions with chain D Water bridges: D:F.21, D:P.22, D:R.23, D:Y.78, D:W.87, D:W.87 GOL.16: 7 residues within 4Å: Chain D: I.29, N.30, T.31, S.33, S.34, P.35, Q.38 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.30, D:S.34 Water bridges: D:P.28, D:Q.38

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

2020-03-11

Peptides

Nucleoprotein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Nucleoprotein