SMTL ID : 5f9o.1

Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235.09 in complex with HIV-1 clade A/E 93TH057 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: E.44, N.45 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.45 NAG.2: 6 residues within 4Å: Chain A: N.118, T.120, I.156, S.158, N.160 Ligands: NAG.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.160 Hydrogen bonds: A:S.158, A:N.160 Water bridges: A:N.118 NAG.3: 3 residues within 4Å: Chain A: H.42, N.113, N.125 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.125 NAG.4: 10 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, L.145, N.146, C.306, V.307, S.308 Ligands: NAG.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:S.308 NAG.5: 5 residues within 4Å: Chain A: N.160, N.163, H.220, F.221 Ligands: NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.221 Hydrogen bonds: A:N.160 NAG.6: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.154, A:N.173, A:Q.212, A:K.216, A:K.216 NAG.7: 3 residues within 4Å: Chain A: N.179, Y.198, E.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.198 Water bridges: A:E.200, A:E.200 NAG.8: 4 residues within 4Å: Chain A: N.202, T.204, K.205, K.208 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain A: K.218, N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.218 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: 6 residues within 4Å: Chain A: Q.256, N.259, T.261, C.262, K.269, C.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.261, A:K.269 NAG.12: 3 residues within 4Å: Chain A: S.175, N.309 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.175 Water bridges: A:S.175, A:S.175

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

EPE.13: 6 residues within 4Å: Chain A: L.9, C.11, H.29, A.30, Q.60, D.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.29 Salt bridges: A:D.64, A:D.64 EPE.14: 5 residues within 4Å: Chain A: R.195, I.281, K.282, Q.283, I.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.283, A:I.284 Salt bridges: A:K.282

1 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.15: 7 residues within 4Å: Chain A: A.17, H.18, E.19, T.20, V.25, T.28, H.29 No protein-ligand interaction detected (PLIP)

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

2016-03-16

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
CH235.9 Heavy chain: B
CH235.09 Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

CH235.9 Heavy chain

CH235.09 Light chain