SMTL ID : 4xmp.1

Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with HIV-1 clade A strain Q842.d12 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 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: H.42, K.113, E.115, N.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.115, A:N.125, 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.244, C.307, E.308, S.309 Ligands: NAG.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:E.95, 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, A.28, I.29, T.30, R.32, H.33, L.92 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.30, C:R.32, C:H.33, A:N.160 Water bridges: C:R.32 NAG.4: 5 residues within 4Å: Chain A: K.177, N.179, N.200, R.306, E.308 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.177, A:K.177 NAG.5: 5 residues within 4Å: Chain A: N.202, T.204, E.205, D.274, T.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.202, A:E.205, A:E.205 NAG.6: 4 residues within 4Å: Chain A: N.207, N.208, H.211, W.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.211 Water bridges: A:N.207 NAG.7: 2 residues within 4Å: Chain A: N.222, H.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.222 NAG.8: 7 residues within 4Å: Chain A: N.229, S.230, T.238, 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:T.254 Water bridges: A:T.254 NAG.9: 5 residues within 4Å: Chain A: N.252, T.254, N.255 Ligands: NAG.8, NAG.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.252 Water bridges: A:N.252, A:N.255, A:N.255 NAG.10: 4 residues within 4Å: Chain A: T.254, 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, L.149, P.175, E.308, S.309, N.310 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.310

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

BU3.12: 15 residues within 4Å: Chain A: W.69, V.139, S.140, T.141, E.236, S.241, F.242, N.243, F.248, Y.250, I.286, N.287, W.289, M.337 Ligands: BU3.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.139, A:T.141 Hydrogen bonds: A:S.241, A:N.287 Water bridges: A:F.242 BU3.13: 11 residues within 4Å: Chain A: E.236, I.237, N.287, M.288, W.289, G.335, D.336, M.337 Chain B: R.54, G.55 Ligands: BU3.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.335, B:R.54

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 VRC08: B
LIGHT CHAIN OF ANTIBODY VRC08: 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 VRC08

LIGHT CHAIN OF ANTIBODY VRC08

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