SMTL ID : 5te4.1

Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade G Strain X2088 gp120 Core

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.118, T.120, S.158, T.224 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.118, A:T.120, A:T.120 NAG.2: 4 residues within 4Å: Chain A: E.44, R.113, N.125, K.151 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.113 Hydrogen bonds: A:E.44, A:E.44 NAG.3: 10 residues within 4Å: Chain A: E.95, P.96, K.136, V.138, L.145, N.146, C.311, I.312, S.313 Ligands: NAG.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:S.313 NAG.4: 7 residues within 4Å: Chain A: N.160, T.162 Chain C: Q.27, G.28, V.29, D.32 Ligands: NAG.1 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:T.162, C:Q.27, C:G.28, C:D.32 NAG.5: 6 residues within 4Å: Chain A: I.181, H.198, N.200, N.279, T.281 Ligands: NAG.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.181 Hydrogen bonds: A:H.198 NAG.6: 4 residues within 4Å: Chain A: T.224, N.226 Chain C: S.26, Q.27 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.26, A:N.226 NAG.7: 4 residues within 4Å: Chain A: N.230, D.330, K.331, E.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.230 NAG.8: 4 residues within 4Å: Chain A: L.242, T.246, N.259, S.261 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.242, A:T.246 Hydrogen bonds: A:S.261 NAG.9: 2 residues within 4Å: Chain A: N.265, T.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.267 NAG.10: 4 residues within 4Å: Chain A: N.200, E.278, N.279 Ligands: NAG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.200, A:E.278, A:E.278 NAG.11: 4 residues within 4Å: Chain A: N.146, P.175, N.314 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.314 NAG.20: 4 residues within 4Å: Chain C: T.20, N.22, S.70, N.72 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.22, C:S.70, C:S.70

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

SO4.12: 5 residues within 4Å: Chain A: R.195, I.286, K.287, Q.288, I.289 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.288, A:Q.288, A:I.289 Salt bridges: A:R.195, A:K.287 SO4.13: 3 residues within 4Å: Chain A: H.100, H.133, G.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.134 Salt bridges: A:H.100 SO4.14: 3 residues within 4Å: Chain A: N.235, R.337 Chain B: R.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.235 Salt bridges: A:R.337 SO4.16: 5 residues within 4Å: Chain B: Y.27, T.28, H.32, R.98, Y.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.28, B:R.98 Salt bridges: B:H.32 SO4.17: 2 residues within 4Å: Chain B: S.7, G.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.8 SO4.19: 4 residues within 4Å: Chain B: K.12, S.17, V.18, R.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.17, B:R.19 Salt bridges: B:K.12 SO4.21: 3 residues within 4Å: Chain C: S.12, K.103, Y.136 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.12, C:S.12, C:Y.136 Salt bridges: C:K.103 SO4.22: 1 residues within 4Å: Chain C: R.207 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.207

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

BU3.15: 9 residues within 4Å: Chain A: W.69, V.139, E.243, S.248, Y.257, V.290, R.291, W.293 Chain B: Y.55 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.69, A:V.139, A:E.243, A:V.290 Hydrogen bonds: A:S.248, A:R.291, B:Y.55

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.18: 1 residues within 4Å: Chain B: R.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.100, B:R.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth. Immunity (2016)

Release Date

2016-11-23

Peptides

HIV-1 clade G strain X2088 gp120: A
Heavy chain of antibody N6: B
Light chain of antibody N6: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

HIV-1 clade G strain X2088 gp120

Heavy chain of antibody N6

Light chain of antibody N6

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