SMTL ID : 5ifa.1

Crystal structure of unbound VRC01c-HuGL2 Fab from an HIV-1 naive donor at 1.82 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-1-1-mer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 1 residues within 4Å: Chain A: S.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.161 SO4.2: 2 residues within 4Å: Chain A: S.137 Chain B: K.209 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.209 SO4.3: 2 residues within 4Å: Chain A: R.85, R.87 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.85, A:R.87

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 3 residues within 4Å: Chain A: V.93, Q.110, G.111 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.93 Water bridges: A:L.113 1PE.5: 5 residues within 4Å: Chain A: S.7, E.10, K.19, S.21, Y.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.10 1PE.6: 3 residues within 4Å: Chain A: D.213, K.214, K.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.214, A:K.215 1PE.7: 4 residues within 4Å: Chain A: K.134 Chain B: S.210, F.211, N.212 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.212, B:N.212, A:K.134

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: R.38, Q.39, A.40, Q.43, G.44, E.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.38, A:A.40 Water bridges: A:G.44 GOL.9: 7 residues within 4Å: Chain A: S.100, S.102, S.104, D.106 Chain B: L.52, Y.55, E.61 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.100, A:S.102, A:S.104, A:D.106, B:E.61 GOL.10: 4 residues within 4Å: Chain A: P.41, V.93, L.113, E.153 No protein-ligand interaction detected (PLIP) GOL.11: 7 residues within 4Å: Chain A: T.165, S.166, G.167, V.168, H.169 Chain B: D.169, K.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.167, A:H.169 GOL.12: 7 residues within 4Å: Chain B: Q.43, K.45, K.51, P.65, F.68, E.87, D.88 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.43, B:K.45, B:K.51, B:K.51, B:E.87 GOL.13: 5 residues within 4Å: Chain B: R.144, E.145, A.146, E.163, L.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.144, B:A.146, B:E.163 GOL.14: 6 residues within 4Å: Chain B: D.153, E.189, K.190, H.191, K.192, R.213 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.189, B:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jardine, J.G. et al., HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen. Science (2016)

Release Date

2016-04-06

Peptides

VRC01c-HuGL2 Fab heavy chain: A
VRC01c-HuGL2 Fab light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

VRC01c-HuGL2 Fab heavy chain

VRC01c-HuGL2 Fab light chain

Related Entries With Identical Sequence