SMTL ID : 4xny.1

Crystal structure of broadly and potently neutralizing antibody VRC08C in complex with HIV-1 clade A strain Q842.d12 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: H.42, K.113, E.115, K.124, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG.2: 13 residues within 4Å: Chain A: E.95, P.96, K.136, V.138, L.145, N.146, F.242, N.243, C.307, E.308, S.309, N.310 Ligands: NAG.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:E.95, A:K.136, A:N.146, A:E.308, A:S.309 NAG.3: 10 residues within 4Å: Chain A: E.159, N.160, T.162 Chain C: I.2, Q.27, A.28, I.29, S.30, H.33, F.92 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.160, C:S.30, C:H.33 NAG.4: 7 residues within 4Å: Chain A: K.177, N.179, N.200, V.201, N.202, R.306, E.308 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.200 Hydrogen bonds: A:K.177, A:N.202, A:R.306 NAG.5: 5 residues within 4Å: Chain A: N.202, T.204, E.205, D.274, T.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.202, A:E.205 NAG.6: 3 residues within 4Å: Chain A: R.203, N.207, W.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.207 NAG.7: 1 residues within 4Å: Chain A: N.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.222 NAG.8: 8 residues within 4Å: Chain A: N.229, S.230, T.238, T.239, N.252, T.254 Ligands: NAG.9, NAG.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.229, A:S.230, A:N.252, A:T.254 NAG.9: 5 residues within 4Å: Chain A: N.252, T.254, N.255 Ligands: NAG.8, NAG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.252 Water bridges: A:N.255 NAG.10: 5 residues within 4Å: Chain A: T.254, N.255, N.258 Ligands: NAG.8, NAG.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.254 Hydrogen bonds: A:N.258 NAG.11: 8 residues within 4Å: Chain A: K.136, N.146, P.175, K.177, E.308, S.309, N.310 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, X. et al., Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell (2015)

Release Date

2015-04-29

Peptides

Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160: A
HEAVY CHAIN OF ANTIBODY VRC08C: B
LIGHT CHAIN OF ANTIBODY VRC08C: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160

HEAVY CHAIN OF ANTIBODY VRC08C

LIGHT CHAIN OF ANTIBODY VRC08C

Related Entries With Identical Sequence