SMTL ID : 6vjn.1

Structure of NHP D11A.B5Fab in complex with 16055 V2b peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-2-mer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: P.33, T.105, A.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.106 NA.2: 2 residues within 4Å: Chain B: Q.57, R.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.57, B:R.59, B:R.59 NA.3: 3 residues within 4Å: Chain B: K.101, S.102, E.103 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.103, B:E.103, B:E.103 Water bridges: B:S.102 NA.4: 1 residues within 4Å: Chain B: T.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.24, B:T.24 NA.5: 4 residues within 4Å: Chain B: Y.117 Chain C: E.6, R.9, S.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.6 Water bridges: C:R.9 NA.6: 5 residues within 4Å: Chain C: E.8, S.14, Y.16 Chain D: S.14, K.15 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.14, D:K.15, C:E.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aljedani, S.S. et al., Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization. Plos Pathog. (2021)

Release Date

2021-01-20

Peptides

D11A.B5 Fab Heavy chain: A
D11A.B5 Fab Light chain: B
V2b peptide: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
G

D
F

D11A.B5 Fab Heavy chain

D11A.B5 Fab Light chain

V2b peptide