SMTL ID : 4laj.4 (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

8 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.186 Water bridges: A:N.184 NAG.2: 5 residues within 4Å: Chain A: N.203, H.222, N.224, R.328 Ligands: NAG.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.203, A:N.224 Hydrogen bonds: A:N.203, A:N.224, A:R.328 NAG.3: 5 residues within 4Å: Chain A: N.142, T.144, P.146, S.182, E.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.144, A:T.144 Water bridges: A:N.142 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.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.162, A:L.169 Hydrogen bonds: A:E.119, A:R.160, A:N.170, A:S.331 Water bridges: A:P.120 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:I.178, A:N.197, A:E.198, A:E.198 NAG.6: 8 residues within 4Å: Chain A: V.201, 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: 8 residues within 4Å: Chain A: V.264, N.278, T.280 Chain C: E.44, S.105, L.106, L.107, Y.108 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:V.264, C:Y.108 Hydrogen bonds: A:N.278, A:N.278, A:T.280, C:E.44, C:E.44, C:Y.108 Water bridges: C:L.107 NAG.8: 6 residues within 4Å: Chain A: R.160, N.170, S.199, N.332 Ligands: NAG.4, EDO.11 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.9: 7 residues within 4Å: Chain A: W.93, 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:W.311, A:Q.312, A:Y.319 EDO.10: 7 residues within 4Å: Chain A: L.97, K.98, C.113, P.114, K.115, G.272, Y.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.113, A:G.272 Water bridges: A:K.115, A:V.116 EDO.11: 5 residues within 4Å: Chain A: V.201, S.330, S.331, N.332 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.330

1 x ACA: 6-AMINOHEXANOIC ACID(Non-covalent)

ACA.12: 4 residues within 4Å: Chain A: D.38, P.122, H.124, R.160 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.38 Water bridges: A:R.160 Salt bridges: A:R.160

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
B

B
C

C
I

HIV-1 YU2 gp120 envelope glycoprotein

CD4-mimetic miniprotein M48U1

Llama single domain antibody, JM4

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