SMTL ID : 6mar.1

HIV-1 Envelope Glycoprotein Clone BG505 delCT N332T in complex with broadly neutralizing antibody Fab PGT151

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-3-3-mer

Ligands

22 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: 5 residues within 4Å: Chain E: N.292, N.293, T.294, D.311, I.313 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain E: N.139, Y.156, L.158, D.311 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain E: R.183, N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain E: K.243, P.282, N.437 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain E: E.78, N.79 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain E: N.143, K.154 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain E: N.353, S.354, T.362, N.376, S.378 Ligands: NAG-NAG-BMA.7, NAG-NAG-BMA.7, NAG-NAG-BMA.7 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain G: N.106, S.108 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain H: N.292, N.293, I.313, G.430 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain H: N.139, Y.156, L.158, D.311 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Y.156 NAG-NAG.15: 3 residues within 4Å: Chain H: R.183, N.188, T.189 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain H: N.253, P.282, N.437 Ligands: NAG-NAG-BMA-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain H: N.376, S.378, P.406 Ligands: NAG-NAG.20, NAG-NAG.20, NAG.45 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain H: N.267, T.269, N.270 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain H: F.142, N.143, K.152, K.154 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain H: N.353, G.356, T.362, S.378 Ligands: NAG-NAG.17, NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain I: N.139, Y.156, S.157, L.158, D.311 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain E: R.299 Chain I: R.183, N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain I: N.253, G.254, P.282, N.437 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain I: N.267, T.269, N.270 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain I: S.141, F.142, N.143, K.152, K.154 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 7 residues within 4Å: Chain I: N.353, S.354, S.355, G.356 Ligands: NAG-NAG-BMA.26, NAG-NAG-BMA.26, NAG-NAG-BMA.26 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.4: 7 residues within 4Å: Chain E: S.200, N.253, N.367, C.368, G.369, C.434, V.435 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.369, E:V.435

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.7: 5 residues within 4Å: Chain E: N.376, S.378, P.406 Ligands: NAG-NAG.9, NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 7 residues within 4Å: Chain I: Q.318, N.353, N.376, S.378, P.406 Ligands: NAG-NAG.29, NAG-NAG.29 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-NAG-GAL-NAG-GAL-MAN-NAG-FUC.10: 14 residues within 4Å: Chain C: D.54, W.56, H.57, V.58, S.71, Y.80, P.106, N.115 Chain F: N.106, I.136 Chain G: G.9, I.10, G.11, A.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.115, C:S.71

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

NAG-NAG-BMA-MAN-NAG-GAL-NAG-MAN-NAG-FUC.11: 11 residues within 4Å: Chain C: R.1, Y.32, Q.101, E.102, P.105 Chain D: K.35, F.60, S.61, G.62 Chain F: E.129, N.132 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.102, C:E.102, D:K.35, D:K.35 NAG-NAG-BMA-MAN-NAG-GAL-NAG-MAN-NAG-FUC.31: 13 residues within 4Å: Chain A: P.28, Y.32, F.100, Q.101, E.102, P.105, R.107 Chain B: E.55, F.60, S.61, G.62 Chain J: K.128, N.132 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.32, A:Q.101, A:E.102, A:E.102, A:R.107, B:G.62

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.21: 9 residues within 4Å: Chain H: N.253, F.366, N.367, C.368, R.433, C.434, V.435, S.436 Ligands: NAG-NAG.16 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.24: 10 residues within 4Å: Chain I: S.200, L.252, N.253, N.367, C.368, G.369, I.428, C.434, V.435, S.436 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.369

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

NAG-NAG-BMA-MAN-NAG-GAL-NAG-GAL-MAN-FUC.30: 18 residues within 4Å: Chain A: R.19, D.54, A.55, W.56, H.57, V.58, V.59, L.69, S.71, R.72, Y.80, P.106, N.115 Chain F: I.10 Chain J: N.106, S.108, Y.133, I.136 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain J Hydrogen bonds: A:S.71, A:R.19, A:S.71, A:R.72 Hydrophobic interactions: J:Y.133, J:I.136

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

NAG.32: 3 residues within 4Å: Chain E: Q.284, N.286, R.433 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: F.343, N.345 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.382 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain E: N.225, T.227, I.268, H.342 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: N.267, T.269, N.270 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain F: N.120 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain F: N.113, S.115 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: E.116, N.120 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain G: N.111, R.112, N.113 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain G: N.132 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain H: Q.284, N.286, R.433 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain H: N.345 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: G.22, S.23 Chain H: E.78, N.79 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain H: N.382 Ligands: NAG-NAG.17 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain H: N.225, T.227, G.228, H.342 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain I: Q.284, N.286, T.322 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain I: N.292, I.313 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain I: N.345 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain I: E.78, N.79 Chain J: G.22, S.23 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain I: N.382 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain I: N.225, S.265, E.266, I.268 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain J: N.113, S.115, E.116 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, L. et al., Differential processing of HIV envelope glycans on the virus and soluble recombinant trimer. Nat Commun (2018)

Release Date

2018-09-26

Peptides

Immunoglobulin G PGT151 Fab, Heavy chain: AC
Immunoglobulin G PGT151, Light chain: BD
Envelope glycoprotein gp160: EHI
Envelope glycoprotein gp160: FGJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

C
H

B
N

D
L

E
A

H
C

I
E

F
B

G
D

J
F

Immunoglobulin G PGT151 Fab, Heavy chain

Immunoglobulin G PGT151, Light chain

Envelope glycoprotein gp160

Envelope glycoprotein gp160

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