SMTL ID : 5f9w.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.118, T.120, S.158, E.159, N.160 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.120, A:N.160 NAG.2: 5 residues within 4Å: Chain A: E.40, H.42, N.113, K.115, N.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40, A:K.115, A:S.127 NAG.3: 11 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, L.145, N.146, 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:K.136, A:N.146, A:R.246, A:S.308 NAG.4: 5 residues within 4Å: Chain A: N.160, H.220, F.221 Chain C: R.30 Ligands: NAG.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.221 Hydrogen bonds: A:N.160, A:H.220, C:R.30 Water bridges: A:N.222 NAG.5: 5 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.154, A:N.173 NAG.6: 5 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200, K.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:Y.198, A:K.303 NAG.7: 2 residues within 4Å: Chain A: N.202, K.205 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain A: N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.223 NAG.9: 3 residues within 4Å: Chain A: M.240, N.253, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.253 NAG.10: 5 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, C.271 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:N.259, A:T.261 NAG.11: 4 residues within 4Å: Chain A: M.268, K.269, G.270, N.272 No protein-ligand interaction detected (PLIP) NAG.12: 5 residues within 4Å: Chain A: K.136, N.146, S.175, N.309 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175, A:N.309 NAG.13: 2 residues within 4Å: Chain A: N.322, T.324 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.324, A:T.324

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.14: 1 residues within 4Å: Chain B: R.219 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.219 PO4.15: 4 residues within 4Å: Chain B: Y.27, T.28, N.31, Y.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:N.31, B:Y.32

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 CH235-lineage antibody CH235: B
Light chain of CH235-lineage antibody CH235: 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 CH235-lineage antibody CH235

Light chain of CH235-lineage antibody CH235

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