SMTL ID : 5f96.1

Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235.12 in complex with HIV-1 clade A/E 93TH057 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 NAG.2: 7 residues within 4Å: Chain A: N.118, T.120, P.122, S.158, N.160, H.220 Ligands: NAG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.158, A:N.160 NAG.3: 4 residues within 4Å: Chain A: E.40, N.113, N.125, S.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.40, A:E.40, A:N.113, A:K.115, A:K.115 NAG.4: 11 residues within 4Å: Chain A: D.95, P.96, V.138, L.145, N.146, N.244, R.246, C.306, V.307, S.308 Ligands: NAG.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:N.146, A:R.246, A:R.246, A:S.308 NAG.5: 4 residues within 4Å: Chain A: N.160, H.220 Chain C: R.30 Ligands: NAG.2 No protein-ligand interaction detected (PLIP) NAG.6: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.154, A:Q.212 NAG.7: 5 residues within 4Å: Chain A: E.177, N.179, T.181, E.200, N.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:T.181, A:Y.198 NAG.8: 2 residues within 4Å: Chain A: N.202, K.205 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.223 NAG.10: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.253 NAG.11: 4 residues within 4Å: Chain A: N.259, T.261, C.262, C.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.271, A:C.271 NAG.12: 5 residues within 4Å: Chain A: K.136, N.146, S.175, N.309 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.146 Hydrogen bonds: A:S.175, A:N.309

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.13: 5 residues within 4Å: Chain A: R.195, I.281, K.282, Q.283, I.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.283, A:I.284 Salt bridges: A:R.195, A:K.282 EPE.14: 6 residues within 4Å: Chain A: A.17, H.18, E.19, T.20, T.28, H.29 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.28 EPE.15: 7 residues within 4Å: Chain C: I.105, K.106, R.107, S.167, K.168, D.169, S.170 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.169, C:S.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonsignori, M. et al., Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody. Cell (2016)

Release Date

2016-03-09

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
HEAVY CHAIN OF ANTIBODY CH235.12: B
LIGHT CHAIN OF ANTIBODY CH235.12: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

HEAVY CHAIN OF ANTIBODY CH235.12

LIGHT CHAIN OF ANTIBODY CH235.12

Related Entries With Identical Sequence