SMTL ID : 8x1h.1

Crystal structure of N-terminal domain of Nucleocapsid protein of SARS-CoV-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-16-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 27 residues within 4Å: Chain A: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain E: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain I: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain M: T.8, A.9, S.10, R.47, Y.68, Y.70 Ligands: GOL.3, GOL.5, GOL.7 20 PLIP interactions: 8 interactions with chain A, 7 interactions with chain M, 3 interactions with chain E, 2 interactions with chain I Hydrogen bonds: A:S.10, A:S.10, A:R.47, A:Y.70, M:S.10, M:R.47, M:Y.70, E:S.10, E:R.47, E:Y.70, I:S.10, I:Y.70 Water bridges: A:S.10, A:S.10, A:S.10, A:S.10, M:A.9, M:A.9, M:A.9, M:A.9 GOL.2: 3 residues within 4Å: Ligands: GOL.4, GOL.6, GOL.8 No protein-ligand interaction detected (PLIP) GOL.3: 27 residues within 4Å: Chain A: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain E: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain I: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain M: T.8, A.9, S.10, R.47, Y.68, Y.70 Ligands: GOL.1, GOL.5, GOL.7 20 PLIP interactions: 8 interactions with chain A, 7 interactions with chain M, 3 interactions with chain E, 2 interactions with chain I Hydrogen bonds: A:S.10, A:S.10, A:R.47, A:Y.70, M:S.10, M:R.47, M:Y.70, E:S.10, E:R.47, E:Y.70, I:S.10, I:Y.70 Water bridges: A:S.10, A:S.10, A:S.10, A:S.10, M:A.9, M:A.9, M:A.9, M:A.9 GOL.4: 3 residues within 4Å: Ligands: GOL.2, GOL.6, GOL.8 No protein-ligand interaction detected (PLIP) GOL.5: 27 residues within 4Å: Chain A: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain E: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain I: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain M: T.8, A.9, S.10, R.47, Y.68, Y.70 Ligands: GOL.1, GOL.3, GOL.7 20 PLIP interactions: 8 interactions with chain A, 7 interactions with chain M, 3 interactions with chain E, 2 interactions with chain I Hydrogen bonds: A:S.10, A:S.10, A:R.47, A:Y.70, M:S.10, M:R.47, M:Y.70, E:S.10, E:R.47, E:Y.70, I:S.10, I:Y.70 Water bridges: A:S.10, A:S.10, A:S.10, A:S.10, M:A.9, M:A.9, M:A.9, M:A.9 GOL.6: 3 residues within 4Å: Ligands: GOL.2, GOL.4, GOL.8 No protein-ligand interaction detected (PLIP) GOL.7: 27 residues within 4Å: Chain A: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain E: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain I: T.8, A.9, S.10, R.47, Y.68, Y.70 Chain M: T.8, A.9, S.10, R.47, Y.68, Y.70 Ligands: GOL.1, GOL.3, GOL.5 20 PLIP interactions: 8 interactions with chain A, 7 interactions with chain M, 3 interactions with chain E, 2 interactions with chain I Hydrogen bonds: A:S.10, A:S.10, A:R.47, A:Y.70, M:S.10, M:R.47, M:Y.70, E:S.10, E:R.47, E:Y.70, I:S.10, I:Y.70 Water bridges: A:S.10, A:S.10, A:S.10, A:S.10, M:A.9, M:A.9, M:A.9, M:A.9 GOL.8: 3 residues within 4Å: Ligands: GOL.2, GOL.4, GOL.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumari, S. et al., Unveiling potential inhibitors targeting the nucleocapsid protein of SARS-CoV-2: Structural insights into their binding sites. Int.J.Biol.Macromol. (2024)

Release Date

2023-11-22

Peptides

Nucleoprotein: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

M
A

N
B

O
C

P
D

Nucleoprotein