SMTL ID : 4lsv.1

Crystal structure of broadly and potently neutralizing antibody 3BNC117 in complex with HIV-1 clade C C1086 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.118, T.120, I.156, S.158 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.118 Hydrogen bonds: A:T.120 NAG.2: 3 residues within 4Å: Chain A: A.44, N.113, N.125 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.44 Hydrogen bonds: A:N.113, A:N.125, A:N.125 NAG.3: 8 residues within 4Å: Chain A: D.95, K.136, V.138, N.146, C.309, N.310, S.311 Ligands: NAG.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.136, A:N.146, A:S.311 NAG.4: 5 residues within 4Å: Chain A: E.159, N.160 Chain C: G.27, Y.28, Y.87 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.28, C:Y.87, A:N.160 NAG.5: 5 residues within 4Å: Chain A: I.154, N.173, E.174, K.212, E.216 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.173, A:E.174 Hydrogen bonds: A:K.212, A:K.212 NAG.6: 5 residues within 4Å: Chain A: N.207, N.208, Q.211, Y.267, N.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.208, A:Y.267 NAG.7: 3 residues within 4Å: Chain A: L.236, N.253, S.255 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.236 Hydrogen bonds: A:N.253, A:S.255 NAG.8: 5 residues within 4Å: Chain A: P.230, D.256, N.259, T.270, R.272 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.230 Hydrogen bonds: A:N.259, A:G.271 NAG.9: 1 residues within 4Å: Chain A: N.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.264 NAG.10: 4 residues within 4Å: Chain A: S.175, N.310, N.312 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.175, A:N.177, A:N.310, A:N.312 NAG.11: 5 residues within 4Å: Chain C: T.20, R.61, W.63, E.66, N.68 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.63 Hydrogen bonds: C:E.66, C:N.68

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.12: 6 residues within 4Å: Chain C: Q.33, K.41, P.55, R.57, E.77, D.78 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.33, C:K.41, C:R.57, C:D.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies. Immunity (2013)

Release Date

2013-08-21

Peptides

envelope glycoprotein GP120: A
HEAVY CHAIN OF ANTIBODY 3BNC117: B
LIGHT CHAIN OF ANTIBODY 3BNC117: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

envelope glycoprotein GP120

HEAVY CHAIN OF ANTIBODY 3BNC117

LIGHT CHAIN OF ANTIBODY 3BNC117

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