SMTL ID : 4laj.3 (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 Compare

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: 6 residues within 4Å: Chain A: N.203, T.205, H.222, N.224, R.328 Ligands: NAG.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.203, A:N.224, A:Q.326, A:R.328, A:R.328 Water bridges: A:N.203, A:T.205 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: 10 residues within 4Å: Chain A: E.119, P.120, R.160, V.162, L.169, N.170, C.329, S.330, S.331 Ligands: NAG.9 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.198 Hydrogen bonds: A:E.177, A:E.177, A:I.178, A:N.197, A:E.198 NAG.6: 7 residues within 4Å: Chain A: N.203, L.225, S.226, N.297, R.328, S.330 Ligands: NAG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.203, A:N.297, A:R.328, A:R.328, A:S.330 NAG.7: 9 residues within 4Å: Chain A: V.264, T.265, N.278, T.280 Chain C: E.44, S.105, L.106, L.107, Y.108 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:V.264, A:T.265, C:Y.108 Hydrogen bonds: A:N.278, A:N.278, C:E.44, C:Y.108 Water bridges: A:T.280 NAG.8: 3 residues within 4Å: Chain A: T.284, N.286, T.288 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: N.170, S.199, N.332 Ligands: NAG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.199, A:N.332 Water bridges: A:S.199, A:S.199

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

EDO.10: 8 residues within 4Å: Chain A: W.93, I.308, M.310, W.311, Q.312, A.317, Y.319 Chain B: X.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.311, A:Q.312, A:Y.319 Water bridges: A:D.94 EDO.11: 3 residues within 4Å: Chain A: D.43, E.45, E.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.43 Water bridges: A:E.45 EDO.12: 5 residues within 4Å: Chain A: V.116, S.117, F.118, G.271, I.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.118, A:F.118

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
A

B
D

C
L

HIV-1 YU2 gp120 envelope glycoprotein

CD4-mimetic miniprotein M48U1

Llama single domain antibody, JM4

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