SMTL ID : 4r4f.1

Crystal structure of non-neutralizing, A32-like antibody 2.2c in complex with HIV-1 YU2 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.184, T.186, N.187 No protein-ligand interaction detected (PLIP) NAG.2: 3 residues within 4Å: Chain A: N.278, T.280, Q.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.281 NAG.3: 3 residues within 4Å: Chain A: N.142, T.144, S.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.144 NAG.4: 5 residues within 4Å: Chain A: R.160, N.170, S.199, N.332 Ligands: NAG.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.199, A:N.332 NAG.5: 3 residues within 4Å: Chain A: N.203, N.297, S.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.203, A:N.297, A:S.330 NAG.6: 9 residues within 4Å: Chain A: E.119, P.120, V.162, L.169, N.170, C.329, S.330, S.331 Ligands: NAG.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.162, A:L.169 Hydrogen bonds: A:E.119, A:S.330, A:S.331, A:S.331 NAG.7: 5 residues within 4Å: Chain A: E.176, E.177, I.178, N.197, Q.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.178 NAG.13: 4 residues within 4Å: Chain C: S.18, S.69, S.78, N.80 No protein-ligand interaction detected (PLIP)

3 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.8: 7 residues within 4Å: Chain A: T.186, N.188, R.340, D.341, G.342, G.343, K.344 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.340 BU3.9: 2 residues within 4Å: Chain B: S.125 Chain C: K.122 No protein-ligand interaction detected (PLIP) BU3.11: 2 residues within 4Å: Chain B: P.58, S.59 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.58 Hydrogen bonds: B:S.59, B:S.59

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

SO4.10: 2 residues within 4Å: Chain C: K.42, R.43 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.43 Salt bridges: C:R.43 SO4.12: 2 residues within 4Å: Chain C: V.1, R.96 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Acharya, P. et al., Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection. J.Virol. (2014)

Release Date

2014-09-17

Peptides

HIV-1 Env gp120: A
Antibody 2.2c LIGHT CHAIN: B
Antibody 2.2c heavy CHAIN: C
M48U1 peptide: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

D
R

HIV-1 Env gp120

Antibody 2.2c LIGHT CHAIN

Antibody 2.2c heavy CHAIN

M48U1 peptide

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