SMTL ID : 6mfp.2 (1 other biounit)

Crystal Structure of the RV305 C1-C2 specific ADCC potent antibody DH677.3 Fab in complex with HIV-1 clade A/E gp120 and M48U1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 3 residues within 4Å: Chain C: N.73, I.76, Y.80 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.76

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

NAG.2: 2 residues within 4Å: Chain A: E.46, N.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.47 NAG.3: 6 residues within 4Å: Chain A: N.120, T.122, G.123, P.124, S.160, L.163 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.163 NAG.4: 3 residues within 4Å: Chain A: H.44, N.115, N.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.44, A:N.115 NAG.5: 10 residues within 4Å: Chain A: D.97, P.98, K.138, V.140, N.148, N.246, R.248, C.308, V.309, S.310 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.140 Hydrogen bonds: A:K.138, A:R.248, A:S.310, A:S.310 NAG.6: 3 residues within 4Å: Chain A: N.162, T.164, N.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.162, A:N.165 NAG.7: 5 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, Q.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.154, A:E.155, A:E.155, A:I.156 NAG.8: 7 residues within 4Å: Chain A: N.181, T.183, Y.200, E.202, K.305, N.307, V.309 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.309 Hydrogen bonds: A:Y.200, A:Y.200, A:N.307 NAG.9: 3 residues within 4Å: Chain A: N.204, T.206, K.207 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204 NAG.10: 3 residues within 4Å: Chain A: M.242, N.255, T.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.255 NAG.11: 4 residues within 4Å: Chain A: Q.258, N.261, T.263, C.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.263, A:C.264 NAG.12: 5 residues within 4Å: Chain A: S.177, E.179, V.309, S.310, N.311 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.309 Hydrogen bonds: A:S.177, A:E.179, A:E.179

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 2 residues within 4Å: Chain A: L.11, D.66 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain D: Q.37, E.45 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Easterhoff, D. et al., Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency. J.Virol. (2020)

Release Date

2019-09-18

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
M48U1 CD4 MIMETIC PEPTIDE: B
DH677.3 Fab heavy chain: C
DH677.3 Fab light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
M

C
C

D
D

clade A/E 93TH057 HIV-1 gp120 core

M48U1 CD4 MIMETIC PEPTIDE

DH677.3 Fab heavy chain

DH677.3 Fab light chain

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