SMTL ID : 4rwy.1

Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC131 in complex with HIV-1 clade B YU2 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 8 residues within 4Å: Chain A: E.183, N.184, T.186 Chain C: G.28, L.29, N.30, S.91 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.30 NAG.2: 8 residues within 4Å: Chain A: N.142, T.144, G.145, P.146, S.182, F.185, Q.244 Ligands: NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.144 NAG.3: 11 residues within 4Å: Chain A: E.119, P.120, R.160, V.162, L.169, N.170, F.268, N.269, C.329, S.330, S.331 6 PLIP interactions: 6 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 NAG.4: 8 residues within 4Å: Chain A: E.175, E.176, E.177, I.178, N.197, E.198, Q.236, K.240 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.198 Hydrogen bonds: A:I.178, A:N.197, A:E.198, A:K.240 NAG.5: 9 residues within 4Å: Chain A: V.201, I.202, N.203, N.224, L.225, S.226, N.297, R.328, S.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.203, A:R.328 NAG.6: 4 residues within 4Å: Chain A: V.264, T.265, N.278, T.280 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.264 Hydrogen bonds: A:T.280

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 5 residues within 4Å: Chain A: R.219, I.304, K.305, Q.306, I.307 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.306, A:Q.306, A:I.307 Water bridges: A:R.303 Salt bridges: A:R.219

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

EDO.8: 10 residues within 4Å: Chain A: E.28, N.73, F.74, N.75, M.76, K.78, N.79, N.80, Y.370, K.371 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.75, A:K.78, A:Y.370 Water bridges: A:N.80 EDO.9: 3 residues within 4Å: Chain B: Q.43, G.44 Chain C: P.99 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.43, B:G.44 EDO.10: 4 residues within 4Å: Chain B: V.161, T.162, V.163, T.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.161, B:T.176 Water bridges: B:V.163 EDO.11: 11 residues within 4Å: Chain B: T.28, F.29, F.32, V.33, I.34, I.51, K.52, R.53, R.71, R.73, V.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.32, B:R.71 EDO.12: 6 residues within 4Å: Chain B: G.8, G.9, K.12, S.17, V.18, T.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.9, B:G.9, B:T.19, B:T.19

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 1 residues within 4Å: Chain B: D.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.219, B:D.219

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 YU2 gp120: A
Antibody 8ANC131 Heavy chain: B
Antibody 8ANC131 Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

HIV-1 YU2 gp120

Antibody 8ANC131 Heavy chain

Antibody 8ANC131 Light chain

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