SMTL ID : 7jln.1

Crystal structure of glVRC01 Fab in complex with anti-idiotype iv9 Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

6 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.1: 4 residues within 4Å: Chain A: K.38, E.46, R.63, F.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.46 NH4.2: 5 residues within 4Å: Chain A: Y.32, R.98, F.100, G.101, Y.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.32, A:R.98, A:F.100 NH4.3: 4 residues within 4Å: Chain A: I.51, S.56, T.71, V.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.56, A:S.56, A:V.72 NH4.4: 4 residues within 4Å: Chain C: Y.33, H.35, N.105, W.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.105 NH4.6: 8 residues within 4Å: Chain C: W.106, D.107 Chain D: Y.32, L.33, A.34, Q.89, Q.90, Y.91 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.91, C:D.107 Water bridges: D:L.33 NH4.7: 7 residues within 4Å: Chain D: Q.37, Q.38, K.39, Q.42, A.43, P.44, R.45 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.39, D:A.43

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain C: G.198, P.221 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seydoux, E. et al., Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies. Cell Rep (2021)

Release Date

2021-03-31

Peptides

iv9 Heavy Chain: A
iv9 Light Chain: B
glVRC01 Heavy Chain: C
glVRC01 Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

iv9 Heavy Chain

iv9 Light Chain

glVRC01 Heavy Chain

glVRC01 Light Chain

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