SMTL ID : 4rx4.2 (1 other biounit)

Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC134 in complex with HIV-1 clade A Q842.d12 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 9 residues within 4Å: Chain A: N.160, T.162, K.166 Chain C: G.28, L.29, N.30, F.31, Y.90, S.91 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.31 Hydrogen bonds: C:N.30, C:N.30, C:N.30, A:T.162, A:K.166 NAG.2: 5 residues within 4Å: Chain A: N.252, T.254, P.279, R.281 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.252 NAG.3: 6 residues within 4Å: Chain A: N.229, T.238, T.239, N.252, T.254 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.229 NAG.4: 4 residues within 4Å: Chain A: K.113, D.114, E.115, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.114, A:N.125 NAG.5: 9 residues within 4Å: Chain A: E.95, P.96, K.136, V.138, N.146, C.307, E.308, S.309, N.310 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.95, A:E.95, A:N.146, A:E.308, A:S.309, A:N.310

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

SO4.6: 4 residues within 4Å: Chain A: R.195, K.283, Q.284, I.285 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.195, A:I.282, A:Q.284, A:I.285 Salt bridges: A:K.283 SO4.8: 4 residues within 4Å: Chain B: Q.3, S.25, Y.27, R.97 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.3 Salt bridges: B:R.97 SO4.9: 6 residues within 4Å: Chain A: T.162, N.164, R.318, D.319 Chain C: S.92, T.93 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:R.318 Hydrogen bonds: C:T.93 SO4.10: 6 residues within 4Å: Chain C: A.9, L.84, P.99, G.100, R.102 Ligands: SO4.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.100 Salt bridges: C:R.102 SO4.11: 3 residues within 4Å: Chain C: R.102, R.141 Ligands: SO4.10 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.141 SO4.12: 3 residues within 4Å: Chain C: R.64, G.65, S.66 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.64, C:G.65

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

EDO.7: 3 residues within 4Å: Chain A: H.100, H.133, G.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell(Cambridge,Mass.) (2015)

Release Date

2015-07-01

Peptides

HIV-1 Clade A Q842.d12 gp120: A
8ANC134 Heavy chain: B
8ANC134 Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
A

C
D

HIV-1 Clade A Q842.d12 gp120

8ANC134 Heavy chain

8ANC134 Light Chain

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