SMTL ID : 4p9h.1

Crystal structure of 8ANC195 Fab in complex with gp120 of 93TH057 HIV-1 and soluble CD4 D1D2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.73 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.179, T.181, Y.198, E.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.198

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2: 22 residues within 4Å: Chain B: N.116, N.118, H.220 Chain C: T.19, W.55, S.57, S.58, A.59, F.63, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.82, S.83, E.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.73, C:A.71

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.3: 12 residues within 4Å: Chain B: E.19, T.20, E.21, S.93, D.95, P.96, V.138, N.146, R.246, C.306, V.307, S.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.20, B:S.93

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.4: 10 residues within 4Å: Chain B: N.160, T.162, N.163 Chain C: Q.1, I.2, H.3, Y.25, G.26, V.27, N.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.1, C:Q.1, C:G.26

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.6: 4 residues within 4Å: Chain B: T.239, M.240, N.253, T.255 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 5 residues within 4Å: Chain B: R.195, K.280, K.282, Q.283, I.284 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.281, B:Q.283, B:I.284 Salt bridges: B:R.195, B:K.280, B:K.282

2 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.8: 6 residues within 4Å: Chain B: A.27, T.28, H.29, A.30, C.31, V.32 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.32 Hydrogen bonds: B:T.28, B:C.31, B:C.31 BEN.9: 1 residues within 4Å: Chain B: V.84 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.84 Hydrogen bonds: B:V.84

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

NAG.10: 3 residues within 4Å: Chain B: N.113, K.115, N.125 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.115, B:N.125 NAG.11: 1 residues within 4Å: Chain B: N.223 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain C: N.88 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scharf, L. et al., Antibody 8ANC195 Reveals a Site of Broad Vulnerability on the HIV-1 Envelope Spike. Cell Rep (2014)

Release Date

2014-05-21

Peptides

T-cell surface glycoprotein CD4: A
Envelope glycoprotein gp160: B
Fab heavy chain: C
Fab light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
G

C
H

D
L

T-cell surface glycoprotein CD4

Envelope glycoprotein gp160

Fab heavy chain

Fab light chain

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