SMTL ID : 8cwk.1

Fab arm of antibodies 4G1-C2 and 10G4 bound to CoV-2 receptor binding domain (RBD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

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

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: D.54, G.55, R.72, D.73, N.74 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.54, A:R.72, A:N.74, A:S.75 GOL.3: 8 residues within 4Å: Chain B: Q.37, K.39, K.45, P.59, R.61, F.62, E.81, D.82 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.37, B:Q.37, B:K.39, B:R.61, B:D.82 GOL.4: 9 residues within 4Å: Chain A: L.145, S.181, L.182, S.183 Chain B: Q.160, S.162, S.176, S.177, T.178 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.181, A:S.181, A:S.183, A:S.183, B:Q.160, B:S.176, B:T.178 GOL.5: 6 residues within 4Å: Chain C: Y.31, S.53, H.54 Chain E: A.16, A.20, N.22 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:S.53, C:S.53, E:A.20 GOL.6: 8 residues within 4Å: Chain D: Q.37, K.45, L.47, P.59, R.61, F.62, E.81, D.82 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.37, D:R.61, D:D.82, D:D.82 GOL.8: 5 residues within 4Å: Chain E: S.43, T.44, G.72, V.75, Y.176 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.44, E:T.44

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

NAG.2: 2 residues within 4Å: Chain B: S.12, N.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.107 NAG.7: 4 residues within 4Å: Chain E: F.6, G.7, F.10, N.11 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.10 Hydrogen bonds: E:N.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2023-05-24

Peptides

Heavy chain of Fab arm of antibody 10G4: A
Light chain of Fab arm of antibody 10G4: B
Heavy chain of Fab arm of antibody 4G1-C2: C
Light chain of Fab arm of antibody 4G1-C2: D
Spike protein S1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

D
B

E
C

Heavy chain of Fab arm of antibody 10G4

Light chain of Fab arm of antibody 10G4

Heavy chain of Fab arm of antibody 4G1-C2

Light chain of Fab arm of antibody 4G1-C2

Spike protein S1

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