SMTL ID : 6olp.1

Full length HIV-1 Env AMC011 in complex with PGT151 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-2-2-mer

Ligands

14 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.129 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.279, T.281, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: M.374, N.387, T.389 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: E.296, N.298, S.336 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: N.304, I.325 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: E.86, N.87 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: L.133, N.159, S.161, K.174, Y.176, E.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.174 NAG-NAG.11: 3 residues within 4Å: Chain A: E.271, N.292, Q.346 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: E.86, N.87 Chain D: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: T.127, N.163 Chain E: M.168 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain C: V.84, N.232, D.233, T.243, N.244 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: N.387, T.389, Q.390 Ligands: NAG.44 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain E: E.86, N.87 Chain F: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain E: E.82, N.232, N.244 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.232, K.234, N.244 No protein-ligand interaction detected (PLIP)

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.6: 8 residues within 4Å: Chain A: P.215, L.264, N.265, N.378, R.438, S.440, S.441 Ligands: NAG-NAG-BMA.8 No protein-ligand interaction detected (PLIP)

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.8: 7 residues within 4Å: Chain A: N.265, L.268, S.294, S.440, S.441, N.442 Ligands: NAG-NAG-BMA-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 8 residues within 4Å: Chain E: V.257, L.264, N.265, N.378, G.380, C.439, S.440, S.441 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.380

1 x NAG- NAG- BMA- MAN- NAG- GAL- NAG- MAN- 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)-[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-FUC.12: 14 residues within 4Å: Chain B: R.122, E.123, N.126 Chain G: V.2, D.26, F.27, P.28, Y.32, R.98, E.102, S.103 Chain H: N.33, F.60, S.61 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:D.26, G:F.27, G:R.98, G:Y.32, G:E.102, G:E.102, G:E.102, H:N.33, H:S.61

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- FUC: 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-MAN-FUC.13: 13 residues within 4Å: Chain B: N.100, S.102, Y.127, L.130 Chain G: R.19, D.54, A.55, W.56, L.69, S.71, R.72, Y.80, P.106 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: G:P.106, B:Y.127 Hydrogen bonds: G:R.19, G:S.71, G:R.72, G:R.72

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

NAG-FUC.14: 1 residues within 4Å: Chain B: N.114 No protein-ligand interaction detected (PLIP) NAG-FUC.19: 4 residues within 4Å: Chain C: V.185, I.187, R.195, N.200 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.188, C:R.195

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.18: 8 residues within 4Å: Chain C: E.63, N.265, N.378, I.433, C.439, S.440, S.441 Ligands: NAG.36 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-MAN-NAG-FUC.21: 15 residues within 4Å: Chain D: E.123, N.126 Chain I: R.1, V.2, Y.32, Q.101, E.102, P.105, R.107 Chain J: K.35, Q.50, F.54, F.60, S.61, G.62 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:Y.32, I:E.102, J:K.35, J:K.35, J:Q.50

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, Y.127 Chain F: G.3, I.4, G.5 Chain I: R.19, D.54, A.55, W.56, H.57, V.58, L.69, S.71, Y.80, P.106 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain D Hydrogen bonds: I:S.71, I:R.19, I:S.71 Hydrophobic interactions: D:Y.127

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

NAG.26: 2 residues within 4Å: Chain A: N.163, V.172 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: R.195, N.200 Chain C: M.168 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.237, T.239, S.277 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: N.298, T.300, H.332, N.334, V.409 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.393 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.191, T.192 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: G.356, N.357 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.363, R.464 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.129, N.191 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.237, T.239 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: S.294, N.442 Ligands: NAG-NAG-BMA-MAN-MAN.18 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.279, T.281, D.282 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.159, Y.176 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.191 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: N.298, N.334, I.335, S.336, R.438 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.304, I.325 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: H.332, N.334, T.407, V.409, R.438 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain C: E.271, V.273, N.292, K.293, Q.346, K.350 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: Q.390, N.393 Ligands: NAG-NAG.20 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.357, K.358 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.363, H.364, I.462, R.464 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain D: N.114 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain E: N.163, Q.173, K.174 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain E: L.133, N.159, L.178 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain E: N.279, T.281, D.282 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain E: E.271, E.272, N.292, K.293, Q.346 Ligand excluded by PLIP NAG.52: 6 residues within 4Å: Chain E: T.300, H.332, N.334, T.407, V.409, R.438 Ligand excluded by PLIP NAG.53: 7 residues within 4Å: Chain E: E.296, N.298, N.334, I.335, S.336, T.407, R.438 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: N.304, Q.436 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain E: Q.390, N.393 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain E: N.363 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain E: N.237, T.239, S.277, A.278, F.280 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain E: N.357, K.358 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain E: N.191 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain E: R.195, N.200, T.201 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain E: N.129 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain E: L.268, S.294, N.442 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain F: N.105, K.106, Q.110 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain F: N.114 Ligand excluded by PLIP NAG.65: 1 residues within 4Å: Chain F: N.126 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain F: N.100, S.102, L.130 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torrents de la Pena, A. et al., Similarities and differences between native HIV-1 envelope glycoprotein trimers and stabilized soluble trimer mimetics. Plos Pathog. (2019)

Release Date

2019-07-31

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: 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
G

I
H

H
I

J
L

Envelope glycoprotein gp120

Envelope glycoprotein gp41

Immunoglobulin G PGT151 Fab, Heavy chain

Immunoglobulin G PGT151 Fab, Light chain

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