SMTL ID : 8cwj.2 (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

2 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: 4 residues within 4Å: Chain A: Y.27 Chain C: D.32, S.34, N.38 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 5 residues within 4Å: Chain C: F.6, G.7, F.10, N.11, V.35 No protein-ligand interaction detected (PLIP)

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain C: Q.77, G.84, R.85 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.77, C:R.85 GOL.4: 3 residues within 4Å: Chain A: S.56, T.58 Chain C: R.76 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.58, A:T.58, C:R.76, C:R.76 GOL.5: 5 residues within 4Å: Chain C: F.10, N.11, S.41, F.42, W.104 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.10, C:N.11, C:S.41 GOL.6: 4 residues within 4Å: Chain C: G.72, V.171, G.172, Y.176 No protein-ligand interaction detected (PLIP) GOL.7: 8 residues within 4Å: Chain C: R.125, E.133, R.134, D.135, S.137 Chain D: S.57, T.58, Y.59 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.125, C:E.133, C:D.135, D:S.57, D:T.58 Water bridges: D:T.58 GOL.12: 4 residues within 4Å: Chain D: G.26, F.27, R.28, N.77 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.26, D:G.26, D:F.27 GOL.14: 7 residues within 4Å: Chain C: Y.117, L.120, F.158, L.160, S.162 Chain E: Q.27, D.28 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:Y.117, C:S.162, E:Q.27 GOL.15: 9 residues within 4Å: Chain C: T.14, F.15, A.16, S.17, N.118, Y.119 Chain E: D.31, Y.32, Y.50 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:Y.32, E:Y.32, C:S.17 Water bridges: C:N.116 GOL.16: 8 residues within 4Å: Chain E: Q.37, K.45, L.47, P.59, R.61, F.62, E.81, D.82 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.37, E:K.45, E:R.61, E:D.82, E:D.82

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

CL.8: 2 residues within 4Å: Chain C: R.23, F.132 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain C: T.83, K.92 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain C: N.128 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain C: G.170 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain D: R.72 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
A

B
B

C
I

D
U

E
V

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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