SMTL ID : 9cpq.1

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-44 and CC12.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

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

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: F.6, G.7, F.10, N.11, V.35 Ligands: CIT.3 No protein-ligand interaction detected (PLIP)

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

CIT.2: 6 residues within 4Å: Chain A: S.43, T.44, G.72, V.75, R.76, Y.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.43, A:T.44, A:T.44, A:R.76 CIT.3: 9 residues within 4Å: Chain A: F.10, N.11, V.35, L.36, S.39, S.41, F.42 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.42 Hydrogen bonds: A:S.39, A:S.41, A:S.41 CIT.4: 12 residues within 4Å: Chain A: G.144, S.145 Chain B: Q.1, S.25, G.26, F.27, T.28 Chain E: Q.153, K.155, E.201, T.203, P.210 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E, 3 interactions with chain B Hydrogen bonds: A:S.145, A:S.145, E:Q.153, B:Q.1, B:S.25, B:G.26 Salt bridges: E:K.151, E:K.155

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

Spike protein S1: A
CC12.3 Fab heavy chain: B
CC12.3 Fab light chain: C
M22-44 Fab heavy chain: D
M22-44 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

C
G

D
H

E
L

Spike protein S1

CC12.3 Fab heavy chain

CC12.3 Fab light chain

M22-44 Fab heavy chain

M22-44 Fab light chain

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