SMTL ID : 7n3d.1

Crystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: L.150, V.178, S.186, L.187, S.188 Chain B: T.178 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.188 Water bridges: A:S.188, B:S.162, B:T.178 EDO.3: 6 residues within 4Å: Chain A: Y.94 Chain B: Q.38, K.39, R.40, G.41, K.42 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.41, B:K.42, B:K.42, A:Y.94 Water bridges: B:Q.38 EDO.4: 7 residues within 4Å: Chain B: Q.37, K.45, P.59, R.61, F.62, E.81, D.82 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.37, B:K.45, B:K.45, B:R.61, B:E.81, B:D.82 Water bridges: B:K.39 EDO.8: 5 residues within 4Å: Chain B: S.31, Y.32, A.50 Chain C: P.79, N.97 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.31, C:N.97 Water bridges: B:S.31, C:Y.80 EDO.9: 5 residues within 4Å: Chain C: W.9, N.32, N.34, I.103, I.114 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.32, C:N.34 EDO.10: 5 residues within 4Å: Chain C: V.29, P.30, Q.40, T.92, P.119 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.29, C:Q.40 Water bridges: C:G.28, C:Q.40, C:T.92 EDO.11: 3 residues within 4Å: Chain C: N.83, K.84, D.85 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.83, C:D.85 Water bridges: C:D.85

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

CL.2: 3 residues within 4Å: Chain A: P.14, T.86, A.87 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: P.59, S.60, R.61 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: Q.27, S.28 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: S.65, G.66, D.70, T.72 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: D.101, H.102 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain C: A.82, N.83 Ligand excluded by PLIP

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

2021-07-07

Peptides

S24-1564 Fab heavy chain: A
S24-1564 Fab light chain: B
Nucleoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

S24-1564 Fab heavy chain

S24-1564 Fab light chain

Nucleoprotein

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