SMTL ID : 6ce0.1

Crystal structure of a HIV-1 clade B tier-3 isolate H078.14 UFO-BG Env trimer in complex with broadly neutralizing Fabs PGT124 and 35O22 at 4.6 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.60 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

3 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: 3 residues within 4Å: Chain A: K.109, S.112, N.113 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.100 Ligands: NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: N.274, I.295, Q.411 Chain F: N.64, G.66 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.66

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

NAG-NAG-BMA.3: 3 residues within 4Å: Chain B: N.144, E.145, S.146 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain B: S.306, T.308, N.309 No protein-ligand interaction detected (PLIP)

2 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: 6 residues within 4Å: Chain B: P.185, N.235, N.348, Q.415, S.416, N.417 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 18 residues within 4Å: Chain A: S.17 Chain B: N.58 Chain C: N.30, F.31, Y.32, H.33, W.50, S.52, P.53, Y.54, D.57, R.110, D.111, G.112, S.113, T.115 Chain D: H.95, N.96 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.33, C:Y.54, C:D.111, C:G.112

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.7: 2 residues within 4Å: Chain B: N.357, T.359 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.9: 12 residues within 4Å: Chain B: E.270, R.299, H.302, N.304, I.382, R.413 Chain E: R.103, I.104, Y.105, G.106 Chain F: N.45, Q.47 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:R.299, B:R.299, E:Y.105, E:R.103, E:R.103

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

NAG.10: 6 residues within 4Å: Chain B: S.127, F.128, N.129, R.142, N.144 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.144 Hydrogen bonds: B:R.142 NAG.11: 3 residues within 4Å: Chain B: E.155, R.165, N.170 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.165, B:N.170 NAG.12: 5 residues within 4Å: Chain B: L.55, N.202, D.203, K.204, N.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.204, B:K.204 NAG.13: 5 residues within 4Å: Chain B: E.248, N.249, T.251, N.252 Ligands: NAG.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.251 NAG.14: 6 residues within 4Å: Chain B: E.241, E.242, V.243, N.262, R.316, K.320 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.242, B:V.243, B:N.262, B:K.320 NAG.15: 4 residues within 4Å: Chain B: N.333, D.426, V.437, R.439 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.437 Hydrogen bonds: B:R.439 NAG.16: 1 residues within 4Å: Chain B: N.363 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain B: N.430 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.430 NAG.18: 1 residues within 4Å: Chain B: N.417 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.417 NAG.19: 4 residues within 4Å: Chain B: K.328, N.433, G.434 Ligands: NAG.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.433 NAG.20: 3 residues within 4Å: Chain B: K.326, N.327 Ligands: NAG.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.326, B:K.326, B:N.327 NAG.21: 2 residues within 4Å: Chain B: K.328, N.367 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.367 NAG.22: 3 residues within 4Å: Chain B: N.207, T.209 Ligands: NAG.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, L. et al., HIV-1 vaccine design through minimizing envelope metastability. Sci Adv (2018)

Release Date

2018-12-05

Peptides

Envelope glycoprotein gp160: A
Envelope glycoprotein gp160: B
35O22 Heavy chain: C
35O22 Light chain: D
PGT124 Heavy chain: E
PGT124 Light chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
G

C
D

D
E

E
H

F
L

Envelope glycoprotein gp160

Envelope glycoprotein gp160

35O22 Heavy chain

35O22 Light chain

PGT124 Heavy chain

PGT124 Light chain

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