SMTL ID : 7n3c.1

Crystal Structure of Human Fab S24-202 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: G.66, H.67, V.68, T.69, Q.82, S.84 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.66, A:T.69, A:Q.82, A:S.84 EDO.2: 5 residues within 4Å: Chain A: S.28, S.31, Y.32, W.104, E.107 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.28, A:S.31, A:Y.32, A:Y.32 EDO.3: 3 residues within 4Å: Chain A: H.67, S.84, S.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.67, A:S.84 Water bridges: A:K.87 EDO.4: 2 residues within 4Å: Chain A: Q.65, G.66 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: S.63, F.64, H.67, W.83, K.87, D.90 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.83, A:K.87 Water bridges: A:R.38, A:R.38, A:R.38 EDO.10: 4 residues within 4Å: Chain A: V.101 Chain B: R.92, L.97 Chain C: T.98 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.92 Water bridges: A:R.50 EDO.11: 4 residues within 4Å: Chain A: T.196 Chain B: S.115, N.138, N.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.115, B:S.115, B:N.138 EDO.15: 3 residues within 4Å: Chain C: T.6, G.73, P.74 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.6 EDO.16: 5 residues within 4Å: Chain C: A.12, L.13, T.14, H.16, Y.129 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.12, C:T.14, C:H.16

12 x IOD: IODIDE ION(Non-functional Binders)

IOD.6: 2 residues within 4Å: Chain A: R.50, N.59 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: S.126 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: P.62 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain B: Q.161 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: E.46, W.47 Chain B: F.99 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain B: F.117, I.118 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain B: P.60, A.61, R.62 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain C: K.22, F.23, P.24 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain C: P.125, K.126 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain C: R.52 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain C: W.9, N.107, N.110, N.111 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain C: R.45, Y.68 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.22: 4 residues within 4Å: Chain C: G.17, K.18, E.19, K.126 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.18, C:E.19, C:K.126 Water bridges: C:G.17

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

S24-202 Fab heavy chain: A
S24-202 Fab light chain: B
Nucleoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

S24-202 Fab heavy chain

S24-202 Fab light chain

Nucleoprotein