SMTL ID : 4rx4.1 (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

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

NAG.1: 12 residues within 4Å: Chain A: E.95, P.96, K.136, V.138, L.145, N.146, F.242, N.243, C.307, E.308, S.309, N.310 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:S.309 NAG.2: 5 residues within 4Å: Chain A: K.177, N.179, T.181, N.200, E.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:N.200, A:E.308 NAG.3: 5 residues within 4Å: Chain A: N.229, N.252, T.254, N.255 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.252 NAG.4: 7 residues within 4Å: Chain A: N.229, S.230, T.238, T.239, N.252, T.254 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.229 NAG.5: 6 residues within 4Å: Chain A: N.160, T.162 Chain C: G.28, L.29, N.30, S.91 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.160, C:N.30, C:N.30 NAG.6: 4 residues within 4Å: Chain A: K.113, D.114, E.115, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.115

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

SO4.7: 6 residues within 4Å: Chain A: D.234, N.287, Q.294 Chain B: D.72, R.73, S.74 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.287, A:N.287, A:Q.294, B:R.73, B:S.74 SO4.11: 4 residues within 4Å: Chain A: R.195, K.283, Q.284, I.285 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.284, A:I.285 Salt bridges: A:R.195 SO4.12: 7 residues within 4Å: Chain A: T.162, N.164, R.318, G.320, G.321, T.323 Chain C: S.92 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.321, C:S.92 Salt bridges: A:R.318 SO4.14: 6 residues within 4Å: Chain C: A.9, L.84, G.100, R.102, R.141 Ligands: SO4.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.100, C:R.102 Salt bridges: C:R.102, C:R.141 SO4.15: 4 residues within 4Å: Chain C: R.102, R.141, E.160 Ligands: SO4.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.160 Salt bridges: C:R.141 SO4.16: 3 residues within 4Å: Chain C: R.64, G.65, S.66 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.65

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

EDO.8: 5 residues within 4Å: Chain A: K.74, P.75, C.76, T.80, A.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.75 EDO.9: 9 residues within 4Å: Chain A: W.53, T.167, D.336, D.339, R.342 Chain B: K.52, R.53, S.54, E.102 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.167, A:D.336, A:D.339, A:R.342, B:K.52, B:R.53 EDO.10: 4 residues within 4Å: Chain A: P.38, H.100, H.133, G.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.134 EDO.13: 8 residues within 4Å: Chain A: S.230, T.231, T.317, D.319, R.331 Chain B: R.56, L.57, M.58 No protein-ligand interaction detected (PLIP)

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
G

B
H

C
L

HIV-1 Clade A Q842.d12 gp120

8ANC134 Heavy chain

8ANC134 Light Chain

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