SMTL ID : 5te7.1

Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade C Strain DU172.17 gp120 Core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EPE.1: 5 residues within 4Å: Chain A: G.166, A.167, L.168, T.169, S.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.169, A:S.170, A:S.170 EPE.15: 11 residues within 4Å: Chain C: T.8, L.9, F.10, C.11, W.26, A.30, Q.60, D.64, S.67, Q.71, Y.101 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.64, C:S.67 Salt bridges: C:D.64, C:D.64

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

EDO.2: 10 residues within 4Å: Chain A: L.150, V.178, S.186, L.187, S.188 Chain B: V.129, Q.156, S.158, S.172, T.174 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.188, A:S.188 Water bridges: A:S.188, A:S.188, B:S.172, B:T.174 EDO.3: 8 residues within 4Å: Chain A: L.45, E.46, W.47, G.61, G.62 Chain B: Y.1, Q.92, F.93 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:Q.92, A:W.47 Water bridges: B:Q.92, A:G.62, C:G.317 EDO.5: 9 residues within 4Å: Chain B: Q.37, H.38, K.39, R.42, A.43, P.44, K.45, A.84 Ligands: EDO.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.37, B:K.39, B:R.42, B:K.45 Water bridges: B:K.39, B:A.43 EDO.6: 10 residues within 4Å: Chain B: Q.37, K.45, L.47, V.58, P.59, R.61, F.62, D.81, D.82 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.45, B:D.81 EDO.7: 10 residues within 4Å: Chain A: K.223 Chain B: P.115, P.116, L.121, Y.182, F.205, N.206, R.207, G.208, E.209 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.208, B:E.209 EDO.16: 10 residues within 4Å: Chain A: Q.54, Y.55, R.72, V.74 Chain C: R.283, M.284, G.287, V.288, G.289, Q.290 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.283, C:M.284, C:M.284, C:G.289 EDO.17: 10 residues within 4Å: Chain C: F.158, N.160, L.161, N.163, N.164, K.166, I.168, F.221, R.314, F.326 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.314

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

NAG.4: 7 residues within 4Å: Chain B: S.7, P.8, R.18, T.20, I.21, N.22, N.72 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.72 NAG.8: 6 residues within 4Å: Chain C: N.118, T.120, G.121, P.122, F.158, E.159 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.158 Hydrogen bonds: C:T.120 NAG.9: 6 residues within 4Å: Chain C: E.40, V.42, N.113, K.115, N.125, S.127 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.115, C:N.125, C:S.127 NAG.10: 13 residues within 4Å: Chain C: D.95, P.96, K.136, V.138, L.145, N.146, F.243, N.244, R.246, C.303, K.304, S.305 Ligands: NAG.14 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.138 Hydrogen bonds: C:N.146, C:S.305 NAG.11: 7 residues within 4Å: Chain C: E.152, E.153, V.154, N.173, E.174, R.212, K.216 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:E.174 Hydrogen bonds: C:V.154, C:N.173, C:E.174, C:R.212 NAG.12: 7 residues within 4Å: Chain C: E.177, N.179, N.200, I.201, S.202, N.271, K.304 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.200 Hydrogen bonds: C:N.179, C:K.304 NAG.13: 3 residues within 4Å: Chain C: N.259, T.261, Y.262 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.261 NAG.14: 7 residues within 4Å: Chain C: N.146, S.175, E.177, K.304, S.305, N.306 Ligands: NAG.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.175

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

2016-11-16

Peptides

Heavy chain of N6: A
Light chain of N6: B
HIV-1 gp120 core: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
G

Heavy chain of N6

Light chain of N6

HIV-1 gp120 core

Related Entries With Identical Sequence