SMTL ID : 6dcq.1

Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-2-2-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 5 residues within 4Å: Chain A: L.153, R.167, N.172, T.173 Chain C: R.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.167

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

NAG-NAG.2: 3 residues within 4Å: Chain A: Y.304, N.306, T.384 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: R.268, N.270, N.306, S.308, T.382, D.415 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.268 NAG-NAG.4: 3 residues within 4Å: Chain A: N.102, S.127, M.165 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: T.100, N.102, N.129 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.358, S.360, P.386 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: A.59, N.60 Chain B: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: S.361, N.364 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: I.106, N.125, L.144, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.102, S.127, F.128, N.129 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: N.102, S.127 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.125, L.144, G.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 7 residues within 4Å: Chain C: N.270, T.272, Y.304, N.306, T.382, R.413 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain C: R.268, N.270, S.308, E.311, R.413 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain C: N.237, P.266, D.415, N.417 Ligands: NAG-NAG-BMA-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: N.276, I.297, G.410 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain C: T.344, N.358, S.360, P.386 Ligands: NAG.44 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 8 residues within 4Å: Chain E: R.268, N.270, N.306, V.307, S.308, T.382, R.413 Ligands: NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain E: N.276, I.297 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain E: T.107, N.125, H.142, G.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain E: K.227, N.237, P.266, N.417 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain E: N.270, Y.304, N.306, R.413 Ligands: NAG-NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain E: T.344, N.358, S.360 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 5 residues within 4Å: Chain E: E.250, N.251, S.253, N.255, A.256 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.256 NAG-NAG.32: 6 residues within 4Å: Chain E: T.100, S.127, F.128, N.129, I.138 Ligands: NAG-NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain E: N.102, S.127, T.163 Ligands: NAG-NAG.32 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.9: 9 residues within 4Å: Chain A: S.184, L.236, N.237, N.349, C.350, P.409, C.414, D.415, S.416 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.415

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.12: 6 residues within 4Å: Chain C: V.151, E.152, R.167, N.172, T.173 Chain E: R.283 No protein-ligand interaction detected (PLIP)

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.19: 11 residues within 4Å: Chain C: S.184, P.187, V.229, L.236, N.237, N.349, G.351, C.414, D.415, S.416 Ligands: NAG-NAG.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.415

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.22: 16 residues within 4Å: Chain D: N.100, S.102, T.130 Chain F: I.4 Chain I: R.19, D.54, A.55, W.56, H.57, V.58, V.59, L.69, S.71, Y.80, P.106, N.115 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:P.106 Hydrogen bonds: I:N.115, I:N.115, I:S.71, I:R.19, I:R.19, I:S.71

2 x NAG- NAG- BMA- MAN- NAG- NAG- MAN- NAG- FUC: 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-NAG-MAN-NAG-FUC.23: 17 residues within 4Å: Chain D: E.123, N.126 Chain I: V.2, D.26, P.28, Y.32, R.98, F.100, Q.101, E.102, R.107, V.124 Chain J: K.35, F.54, N.58, F.60, S.61 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:E.102, J:K.35 NAG-NAG-BMA-MAN-NAG-NAG-MAN-NAG-FUC.34: 15 residues within 4Å: Chain F: E.123, N.126 Chain G: V.2, D.26, P.28, Y.32, F.100, Q.101, E.102, S.103, R.107 Chain H: K.35, F.54, F.60, S.61 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:R.107, G:Q.101, H:K.35, H:K.35

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.27: 10 residues within 4Å: Chain E: E.186, L.236, N.237, N.349, G.351, C.414, D.415, S.416 Chain J: K.24, D.75 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:K.24, J:D.75, J:D.75

1 x NAG- NAG- BMA- MAN- NAG- GAL- NAG- GAL- 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)-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-FUC.35: 19 residues within 4Å: Chain B: I.4 Chain F: N.100, S.102, Y.127, T.130 Chain G: D.54, A.55, W.56, H.57, V.58, V.59, L.69, S.71, R.72, Y.80, E.82, P.105, P.106, N.115 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:P.105, F:Y.127, G:A.55 Hydrogen bonds: G:N.115, G:S.71, G:S.71, G:R.72, G:E.82

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

NAG.36: 2 residues within 4Å: Chain A: P.266, N.417 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: N.209, H.326 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.328 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.276, I.297 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.105 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: K.122, E.123, N.126 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.114 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.328 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: S.360, S.361, N.364 Ligands: NAG-NAG.21 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.251, N.255, K.257 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.209, T.211, C.249, I.252 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: A.59, N.60 Chain D: G.16, S.17 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain D: N.105 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: E.110, N.114 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain E: N.328 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: A.59, N.60 Chain F: S.17 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain E: N.364 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain E: N.209, T.211 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain A: R.283 Chain E: R.167, N.172, T.173 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain F: N.114 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain F: N.105 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rantalainen, K. et al., Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design. Cell Rep (2018)

Release Date

2018-06-27

Peptides

Envelope glycoprotein gp160: ACE
Envelope glycoprotein gp160: BDF
Immunoglobulin G PGT151 Fab, Heavy chain: GI
Immunoglobulin G PGT151 Fab, Light chain: HJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

I
M

H
L

J
N

Envelope glycoprotein gp160

Envelope glycoprotein gp160

Immunoglobulin G PGT151 Fab, Heavy chain

Immunoglobulin G PGT151 Fab, Light chain

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