SMTL ID : 6ulc.1

Structure of full-length, fully glycosylated, non-modified HIV-1 gp160 bound to PG16 Fab at a nominal resolution of 4.6 Angstrom

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- GAL: beta-D-galactopyranose-(1-4)-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)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL.1: 5 residues within 4Å: Chain A: N.133, I.134 Chain G: K.77, H.79, W.84 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.79 Hydrophobic interactions: G:W.84

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.2: 12 residues within 4Å: Chain A: D.129, N.159, K.170 Chain G: I.123, Y.130, Y.140, H.141 Chain H: G.50, F.51, D.52, S.53, D.71 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:Y.140, G:Y.140, H:G.50 NAG-NAG-BMA-MAN-MAN.3: 4 residues within 4Å: Chain A: R.194, N.199, T.200 Chain C: R.310 No protein-ligand interaction detected (PLIP)

16 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.4: 7 residues within 4Å: Chain A: P.214, R.254, N.264, R.438, C.439, E.440, S.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.438, A:E.440 NAG-NAG-BMA.6: 6 residues within 4Å: Chain A: S.145, S.146, N.385, S.387 Ligands: NAG-NAG.5, NAG-NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.146 NAG-NAG-BMA.9: 1 residues within 4Å: Chain C: N.137 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 7 residues within 4Å: Chain C: S.131, I.134, T.135, N.136, N.155, Y.172, D.322 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.135 Hydrogen bonds: C:Y.172 NAG-NAG-BMA.14: 5 residues within 4Å: Chain C: N.362, S.363, G.365, F.390 Ligands: NAG.61 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 1 residues within 4Å: Chain E: N.137 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 3 residues within 4Å: Chain E: N.144, S.145 Ligands: NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 5 residues within 4Å: Chain E: N.236, I.274, R.275, S.276, E.352 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 8 residues within 4Å: Chain E: E.213, R.254, N.264, N.376, C.377, E.440, S.441 Ligands: NAG.73 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.213 NAG-NAG-BMA.23: 5 residues within 4Å: Chain E: T.295, N.297, N.333, E.440 Ligands: NAG-NAG-BMA.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 6 residues within 4Å: Chain E: I.142, H.331, C.332, N.333, T.409 Ligands: NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 4 residues within 4Å: Chain E: N.355, T.356 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 8 residues within 4Å: Chain E: S.146, N.385, S.387, F.390, R.413 Ligands: NAG-NAG-BMA.17, NAG-NAG.26, NAG-NAG.26 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.146, E:S.146, E:N.391 NAG-NAG-BMA.28: 4 residues within 4Å: Chain E: H.396, N.397 Ligands: NAG-NAG-BMA.25, NAG-NAG-BMA.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 3 residues within 4Å: Chain E: K.403, P.404, N.405 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 3 residues within 4Å: Chain H: T.24, N.42, T.91 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.5: 5 residues within 4Å: Chain A: N.362, S.363, T.371 Ligands: NAG-NAG-BMA.6, NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.101 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: E.124, S.126, N.127, Y.128 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.144, S.146, N.148 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 12 residues within 4Å: Chain C: P.214, R.254, V.256, L.263, N.264, N.376, C.377, G.378, R.438, C.439, E.440 Ligands: NAG.64 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.378, C:E.440, C:E.440 NAG-NAG.15: 1 residues within 4Å: Chain E: N.133 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 8 residues within 4Å: Chain E: D.129, I.134, T.135, N.155, C.156, S.157, Y.172, D.322 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.135 NAG-NAG.20: 3 residues within 4Å: Chain E: R.194, N.199, T.200 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain E: N.362, S.363, T.371, S.387 Ligands: NAG-NAG-BMA.27, NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain F: S.126, N.127 No protein-ligand interaction detected (PLIP)

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: 5 residues within 4Å: Chain C: T.127, L.128, D.129, N.159, K.170 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.127, C:D.129, C:D.129, C:D.129

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 16 residues within 4Å: Chain E: T.127, L.128, D.129, S.157, N.159 Chain G: E.21, R.117, W.124, H.125, D.127, D.144 Chain H: D.71, H.74, R.75, S.77, G.78 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:S.77, H:G.78, G:R.117, G:D.144, G:D.144

1 x NAG- NAG- BMA- FUC: 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-FUC.31: 11 residues within 4Å: Chain A: D.129, S.131, T.135, N.155, S.157, Y.172, D.322 Chain G: K.50, D.73, M.75, F.133 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: G:F.133, A:T.135, A:D.322 Hydrogen bonds: A:Y.172

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

NAG.33: 4 residues within 4Å: Chain A: N.87 Chain B: A.16, G.17, S.18 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: N.137, I.138, D.326, R.328 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: T.143, N.144 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.187 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.236 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain A: Y.84, E.86, N.231, D.232, K.242, N.243 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.278 Ligand excluded by PLIP NAG.40: 6 residues within 4Å: Chain A: G.270, V.272, N.291, E.292, Q.345, Q.349 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain A: T.295, I.296, N.297, E.440 Ligands: NAG.43 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: N.303, I.324, V.436 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain A: N.297, H.331, N.333, R.438 Ligands: NAG.41 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain A: N.355, T.356, H.396 Ligands: NAG.46 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain A: N.393, T.395, H.396 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain A: T.356, H.396, N.397 Ligands: NAG.44 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain A: K.403, N.405 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain A: N.442 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain A: W.354, N.457, E.458 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain B: K.107, E.111, N.115 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: E.86, N.87 Chain D: S.18 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain C: S.131, Y.132, N.133, I.134, T.135 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: R.194, N.199, T.200 Chain E: R.310 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.236 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: N.278, T.280 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain C: G.270, K.271, V.272, N.291, Q.345 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain C: T.295, I.296, N.297, C.439, E.440 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain C: N.303, N.304, T.305, I.324 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain C: N.297, H.331, N.333, R.438 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain C: N.355 Ligand excluded by PLIP NAG.61: 5 residues within 4Å: Chain C: V.147, N.385, S.387 Ligands: NAG-NAG-BMA.14, NAG-NAG-BMA.14 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain C: I.359, N.393, T.395 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain C: M.402, K.403, N.405 Ligand excluded by PLIP NAG.64: 5 residues within 4Å: Chain C: R.254, N.264, T.293, N.442 Ligands: NAG-NAG.13 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain D: N.101, S.103 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain E: E.86, N.87 Chain F: G.17, S.18 Ligand excluded by PLIP NAG.67: 3 residues within 4Å: Chain E: N.187 Chain G: G.45, F.46 Ligand excluded by PLIP NAG.68: 6 residues within 4Å: Chain E: Y.84, N.231, D.232, K.233, K.242, N.243 Ligand excluded by PLIP NAG.69: 2 residues within 4Å: Chain E: N.278, N.281 Ligand excluded by PLIP NAG.70: 4 residues within 4Å: Chain E: K.271, V.272, N.291, Q.345 Ligand excluded by PLIP NAG.71: 3 residues within 4Å: Chain E: N.303, N.304, Q.434 Ligand excluded by PLIP NAG.72: 4 residues within 4Å: Chain E: F.390, N.391, S.392, N.393 Ligand excluded by PLIP NAG.73: 5 residues within 4Å: Chain E: R.254, N.264, T.293, N.442 Ligands: NAG-NAG-BMA.22 Ligand excluded by PLIP NAG.74: 2 residues within 4Å: Chain E: N.457, E.458 Ligand excluded by PLIP NAG.75: 3 residues within 4Å: Chain F: N.101, S.102, S.103 Ligand excluded by PLIP NAG.76: 3 residues within 4Å: Chain F: E.111, E.114, N.115 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, J. et al., Cryo-EM Structure of Full-length HIV-1 Env Bound With the Fab of Antibody PG16. J.Mol.Biol. (2020)

Release Date

2020-04-29

Peptides

envelope glycoprotein gp120,envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
antibody PG16 Fab heavy chain: G
antibody PG16 Fab light chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

H
L

envelope glycoprotein gp120,envelope glycoprotein gp120

Envelope glycoprotein gp41

antibody PG16 Fab heavy chain

antibody PG16 Fab light chain

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