SMTL ID : 4laj.2 (3 other biounits)

Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, JM4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.184, T.186, N.187 No protein-ligand interaction detected (PLIP) NAG.2: 5 residues within 4Å: Chain A: N.142, T.144, S.182, E.183 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.144 NAG.3: 3 residues within 4Å: Chain A: N.137, K.139, N.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.137 NAG.4: 9 residues within 4Å: Chain A: E.119, P.120, V.162, L.169, N.170, C.329, S.330, S.331 Ligands: NAG.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.162, A:L.169 Hydrogen bonds: A:N.170, A:S.331 Water bridges: A:R.160, A:R.160 NAG.5: 7 residues within 4Å: Chain A: E.176, E.177, I.178, N.197, E.198, Q.236, K.240 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.198 Hydrogen bonds: A:I.178, A:N.197, A:E.198 NAG.6: 8 residues within 4Å: Chain A: V.201, N.203, N.224, L.225, S.226, N.297, R.328, S.330 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.297, A:R.328, A:R.328, A:S.330 NAG.7: 8 residues within 4Å: Chain A: V.264, N.278, T.280 Chain C: E.44, S.105, L.106, L.107, Y.108 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.108, A:V.264 Hydrogen bonds: C:E.44, C:Y.108, A:N.278 Water bridges: C:S.105, C:S.105 NAG.8: 5 residues within 4Å: Chain A: R.160, N.170, S.199, N.332 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.199, A:N.332 Water bridges: A:S.199 NAG.9: 7 residues within 4Å: Chain A: D.138, K.140, F.141, N.142, P.146, T.148 Ligands: NAG.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.148 Hydrogen bonds: A:D.138, A:D.138, A:N.142 Water bridges: A:K.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Acharya, P. et al., Heavy Chain-Only IgG2b Llama Antibody Effects Near-Pan HIV-1 Neutralization by Recognizing a CD4-Induced Epitope That Includes Elements of Coreceptor- and CD4-Binding Sites. J.Virol. (2013)

Release Date

2013-08-14

Peptides

HIV-1 YU2 gp120 envelope glycoprotein: A
CD4-mimetic miniprotein M48U1: B
Llama single domain antibody, JM4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
M

HIV-1 YU2 gp120 envelope glycoprotein

CD4-mimetic miniprotein M48U1

Llama single domain antibody, JM4

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