SMTL ID : 9cps.1

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-91 and CC12.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

8 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 8 residues within 4Å: Chain A: W.47, Y.52, F.58, D.101 Chain B: S.94, P.95, R.96 Ligands: CIT.5 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.94, A:Y.52, A:Y.52 Salt bridges: B:R.96 Hydrophobic interactions: A:F.58 CIT.2: 7 residues within 4Å: Chain A: F.99, Y.103, D.105, Y.106 Chain B: L.46, Y.49, T.56 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.97, A:Y.106, B:T.56, B:T.56, B:T.56 CIT.3: 3 residues within 4Å: Chain A: S.17, Q.81, N.83 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.17, A:S.17, A:Q.81, A:N.83 CIT.4: 3 residues within 4Å: Chain A: K.218 Chain B: N.210, R.211 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.218, A:K.218 CIT.5: 8 residues within 4Å: Chain A: Y.52, D.101, F.102 Chain B: Y.91, G.92, S.93, S.94 Ligands: CIT.1 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.91, B:G.92, B:S.94, A:Y.52 Hydrophobic interactions: A:F.102 CIT.6: 6 residues within 4Å: Chain B: G.9, T.10, Q.100, G.101, K.103, R.142 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.103, B:K.103 Hydrogen bonds: B:Y.87 Salt bridges: B:K.103, B:R.142 CIT.8: 7 residues within 4Å: Chain B: R.108, T.109 Chain D: K.123, G.124, P.125, S.126, T.211 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:S.209, D:T.211 Salt bridges: D:K.123, B:R.108, B:R.108 CIT.9: 1 residues within 4Å: Chain D: K.207 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.207 Salt bridges: D:K.207, D:K.207

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.7: 4 residues within 4Å: Chain C: G.7, F.10, N.11, V.35 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, Z. et al., Structures of CR3022-like antibodies. To Be Published

Release Date

2025-06-25

Peptides

CC12.3 Fab heavy chain: A
CC12.3 Fab light chain: B
Spike protein S1: C
M22-91 Fab heavy chain: D
M22-91 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
A

D
H

E
L

CC12.3 Fab heavy chain

CC12.3 Fab light chain

Spike protein S1

M22-91 Fab heavy chain

M22-91 Fab light chain

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