SMTL ID : 6xsn.1

Crystal structure of NHP VD20.5A4 Fab in complex with 16055 V1V2 1FD6 scaffold

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 2 residues within 4Å: Chain A: Q.1, G.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.1 SCN.3: 5 residues within 4Å: Chain A: Q.39, V.93, F.95 Chain B: G.41, K.42 No protein-ligand interaction detected (PLIP) SCN.6: 6 residues within 4Å: Chain B: S.12, E.105, I.106, Y.140, R.142, Y.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.12, B:Y.173

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: L.149, P.175, V.177, S.185, L.186, S.187 Chain B: S.162, S.176, T.178 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.175, A:S.185, A:S.187, B:S.176 EDO.4: 2 residues within 4Å: Chain B: S.59, R.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.59, B:S.60, B:R.61 EDO.5: 3 residues within 4Å: Chain B: P.8, S.9, S.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.9 EDO.7: 6 residues within 4Å: Chain B: Q.38, K.39, P.40, G.41, T.85, E.165 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:Q.39 Hydrogen bonds: B:Q.38, B:G.41, B:T.85, B:T.85

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

NA.8: 5 residues within 4Å: Chain A: Y.104 Chain B: E.32, D.91 Chain C: E.66, E.67 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.32, B:D.91

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

NAG.9: 4 residues within 4Å: Chain C: V.17, N.18, N.36, Y.53 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.36

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

2021-07-21

Peptides

VD20.5A4_heavy_chain: A
VD20.5A4_light_chain: B
16055_V1V2-1FD6: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

VD20.5A4_heavy_chain

VD20.5A4_light_chain

16055_V1V2-1FD6

Related Entries With Identical Sequence