SMTL ID : 8cwj.1 (1 other biounit)

Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain (pRBD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

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

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 5 residues within 4Å: Chain C: F.6, G.7, N.11, V.35 Ligands: GOL.3 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.38, S.63, F.64, Q.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.38, A:R.38 Water bridges: A:E.46, A:K.87 GOL.3: 6 residues within 4Å: Chain C: F.10, N.11, S.41, F.42, W.104 Ligands: NAG-NAG-FUC.1 No protein-ligand interaction detected (PLIP) GOL.5: 5 residues within 4Å: Chain C: G.72, V.75, V.171, G.172, Y.176 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.176 Water bridges: C:G.72, C:V.75 GOL.9: 5 residues within 4Å: Chain D: S.25, G.26, F.27, R.28, N.77 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.26, D:F.27 GOL.10: 6 residues within 4Å: Chain D: Y.60, K.65, G.66, R.67, F.68, T.69 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.66, D:G.66 GOL.12: 9 residues within 4Å: Chain E: Q.37, K.39, K.45, L.47, P.59, R.61, F.62, E.81, D.82 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:Q.37, E:K.39, E:K.45, E:K.45, E:R.61, E:E.81, E:D.82

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

NAG.4: 3 residues within 4Å: Chain A: Y.27 Chain C: S.34, N.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.38

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

CL.6: 2 residues within 4Å: Chain C: R.85, Y.121 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain C: N.128 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain C: R.125, S.127, N.128, E.133 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain D: T.58 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain E: V.19, T.20 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Langley, D.B. et al., Neutralization of CoV-2 omicron lineages by affinity-matured class 5 antibodies. To Be Published

Release Date

2023-05-24

Peptides

Heavy chain of CR3022 antibody Fab: A
Light chain of CR3022 antibody Fab: B
Spike glycoprotein: C
Heavy chain of 4C12-B12 antibody Fab: D
Light chain of 4C12-B12 antibody Fab: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
G

D
J

E
K

Heavy chain of CR3022 antibody Fab

Light chain of CR3022 antibody Fab

Spike glycoprotein

Heavy chain of 4C12-B12 antibody Fab

Light chain of 4C12-B12 antibody Fab

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