SMTL ID : 6pwu.1

Structure of full-length, fully glycosylated, non-modified HIV-1 gp160 bound to PG16 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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: 8 residues within 4Å: Chain A: N.133 Chain D: K.77, H.79, D.81, W.84 Chain E: R.115, H.117 Ligands: NAG-NAG-BMA-FUC.31 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:R.115, D:H.79, D:H.79, D:D.81

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: 10 residues within 4Å: Chain A: D.129, N.159, K.170 Chain B: D.166 Chain D: I.123, Y.130, H.141 Chain E: F.51, D.52, S.53 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 3 residues within 4Å: Chain A: R.194, N.199, T.200 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: 11 residues within 4Å: Chain A: E.213, P.214, R.254, V.256, L.263, N.264, R.438, C.439, E.440, S.441 Ligands: NAG.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.438, A:E.440 NAG-NAG-BMA.6: 8 residues within 4Å: Chain A: S.146, N.385, S.387, F.390, P.411 Ligands: NAG-NAG.5, NAG-NAG.5, NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 1 residues within 4Å: Chain B: N.137 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 7 residues within 4Å: Chain B: S.131, I.134, T.135, N.155, C.156, S.157, Y.172 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.135 NAG-NAG-BMA.14: 5 residues within 4Å: Chain B: N.362, S.363, T.371, F.390 Ligands: NAG.61 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 1 residues within 4Å: Chain C: N.137 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 2 residues within 4Å: Chain C: N.144 Ligands: NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 4 residues within 4Å: Chain C: W.95, N.236, T.238, S.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 9 residues within 4Å: Chain C: P.214, R.254, V.256, N.264, C.377, R.438, C.439, E.440 Ligands: NAG.73 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 7 residues within 4Å: Chain C: T.295, N.297, N.333, V.334, S.335, R.438, E.440 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 6 residues within 4Å: Chain C: I.142, R.328, H.331, C.332, N.333, T.409 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.328, C:R.328 NAG-NAG-BMA.25: 3 residues within 4Å: Chain C: N.355, T.356 Ligands: NAG-NAG-BMA.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 8 residues within 4Å: Chain C: S.146, N.385, S.387, F.390, R.413 Ligands: NAG-NAG-BMA.17, NAG-NAG.26, NAG-NAG.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.146, C:S.146 NAG-NAG-BMA.28: 4 residues within 4Å: Chain C: T.356, H.396, N.397 Ligands: NAG-NAG-BMA.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 3 residues within 4Å: Chain C: K.403, P.404, N.405 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 2 residues within 4Å: Chain E: 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: 2 residues within 4Å: Chain A: N.606, S.608 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: K.628, E.629, S.631, N.632 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.144, M.149 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 11 residues within 4Å: Chain B: P.214, R.254, V.256, L.263, N.264, N.376, C.377, G.378, R.438, E.440 Ligands: NAG.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.378, B:E.440, B:E.440 NAG-NAG.15: 3 residues within 4Å: Chain C: N.133 Ligands: NAG-NAG.18, NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 7 residues within 4Å: Chain C: S.131, T.135, N.155, C.156, S.157, Y.172 Ligands: NAG-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain A: R.310 Chain C: V.181, R.194, N.199, T.200 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain C: N.362, T.371, S.387 Ligands: NAG-NAG-BMA.27, NAG-NAG-BMA.27, NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain C: S.631, N.632 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 B: T.127, N.159, N.168, R.169, K.170 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.159

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: 13 residues within 4Å: Chain C: T.127, D.129, S.157, F.158, N.159 Chain D: R.117, W.124, D.127 Chain E: F.70, D.71, H.74, S.77, G.78 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: E:S.77, E:G.78, D:R.117, C:D.129

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: 12 residues within 4Å: Chain A: D.129, S.131, T.135, N.155, C.156, S.157, Y.172, D.322 Chain D: D.73, M.75, F.133 Ligands: NAG-NAG-BMA-MAN-NAG-GAL.1 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:D.73, A:D.322, A:D.322 Hydrophobic interactions: A:Y.172, D:F.133, A:T.135

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

NAG.33: 5 residues within 4Å: Chain A: N.87, T.520, A.521, G.522, S.523 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.137 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: T.143, N.144 Ligands: NAG-NAG-BMA.6 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: G.186, N.187 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: N.236, T.238, S.276 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain A: Y.84, N.231, D.232, K.233, N.243 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.278, T.280, N.281 Ligand excluded by PLIP NAG.40: 7 residues within 4Å: Chain A: G.270, K.271, V.272, N.291, E.292, Q.345, Q.349 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain A: T.295, I.296, N.297, S.335, R.438, E.440 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain A: N.303, N.304, T.305, G.435, V.436 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain A: N.297, H.331, N.333, T.409, R.438 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: 4 residues within 4Å: Chain A: I.358, I.359, N.393, T.395 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: 5 residues within 4Å: Chain A: R.254, N.264, T.293, N.442 Ligands: NAG-NAG-BMA.4 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain A: N.457, E.458 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain A: N.620 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain B: N.87, G.522, S.523 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain B: Y.132, N.133, I.134, T.135 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain B: R.194, N.199 Chain C: R.310 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain B: W.95, N.236, T.238, S.276 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain B: N.278, T.280 Ligand excluded by PLIP NAG.56: 6 residues within 4Å: Chain B: G.270, K.271, V.272, N.291, Q.345, Q.349 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain B: T.295, I.296, N.297, R.438, E.440 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain B: N.303, N.304, T.305, I.324 Ligand excluded by PLIP NAG.59: 5 residues within 4Å: Chain B: N.297, H.331, N.333, T.409, R.438 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain B: N.355 Ligand excluded by PLIP NAG.61: 7 residues within 4Å: Chain B: S.145, S.146, V.147, T.372, N.385, S.387 Ligands: NAG-NAG-BMA.14 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain B: S.392, N.393, T.395 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain B: R.341, K.403, N.405 Ligand excluded by PLIP NAG.64: 5 residues within 4Å: Chain B: R.254, N.264, T.293, N.442 Ligands: NAG-NAG.13 Ligand excluded by PLIP NAG.65: 1 residues within 4Å: Chain B: N.606 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain C: N.87, A.521, G.522, S.523 Ligand excluded by PLIP NAG.67: 2 residues within 4Å: Chain C: N.187, N.188 Ligand excluded by PLIP NAG.68: 5 residues within 4Å: Chain C: Y.84, N.231, D.232, K.233, N.243 Ligand excluded by PLIP NAG.69: 2 residues within 4Å: Chain C: N.278, T.280 Ligand excluded by PLIP NAG.70: 6 residues within 4Å: Chain C: G.270, K.271, V.272, N.291, Q.345, Q.349 Ligand excluded by PLIP NAG.71: 5 residues within 4Å: Chain C: N.303, N.304, T.305, I.324, Q.434 Ligand excluded by PLIP NAG.72: 4 residues within 4Å: Chain C: K.361, N.391, S.392, N.393 Ligand excluded by PLIP NAG.73: 5 residues within 4Å: Chain C: R.254, N.264, T.293, N.442 Ligands: NAG-NAG-BMA.22 Ligand excluded by PLIP NAG.74: 3 residues within 4Å: Chain C: W.354, N.457, E.458 Ligand excluded by PLIP NAG.75: 3 residues within 4Å: Chain C: N.606, S.607, S.608 Ligand excluded by PLIP NAG.76: 2 residues within 4Å: Chain C: E.619, N.620 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

2020-02-26

Peptides

Envelope glycoprotein gp160: ABC
Antibody PG16 Fab heavy chain: D
Antibody PG16 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
H

E
L

Envelope glycoprotein gp160

Antibody PG16 Fab heavy chain

Antibody PG16 Fab light chain

Related Entries With Identical Sequence