SMTL ID : 4yfl.2 (1 other biounit)

Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 1B2530 in complex with HIV-1 clade A/E 93TH057 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.39 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: E.44, N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 NAG.2: 6 residues within 4Å: Chain A: N.118, T.120, S.158, E.159, N.160, L.161 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.120 Hydrogen bonds: A:N.118, A:T.120 NAG.3: 3 residues within 4Å: Chain A: N.113, K.115, N.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.113, A:N.113, A:K.115 NAG.4: 7 residues within 4Å: Chain A: N.160, T.162 Chain B: I.110 Chain C: Y.33, Y.92, S.94, D.95 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.94, C:D.95, A:T.162, A:T.162 NAG.5: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.153, A:E.153, A:I.154, A:N.173 NAG.6: 6 residues within 4Å: Chain A: N.179, T.181, Y.198, K.303, N.305, V.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:K.303, A:N.305 NAG.7: 5 residues within 4Å: Chain A: N.202, T.204, K.205, G.273, T.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.202, A:K.205, A:T.274 NAG.8: 5 residues within 4Å: Chain A: L.236, T.239, M.240, N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.236 Hydrogen bonds: A:N.253 NAG.9: 7 residues within 4Å: Chain A: Q.256, N.259, T.261, C.262, M.268, G.270, C.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.259 NAG.10: 7 residues within 4Å: Chain A: T.204, C.262, E.266, T.267, M.268, C.271, N.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.268, A:M.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell (2015)

Release Date

2015-06-03

Peptides

Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160: A
1B2530 heavy chain: B
1B2530 Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
I

Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160

1B2530 heavy chain

1B2530 Light chain

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