SMTL ID : 5u7m.1

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-378806 in Complex with Human Antibodies PGT122 and 35O22 at 3.8 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

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.1: 19 residues within 4Å: Chain A: G.16, S.17 Chain B: N.30, F.31, H.33, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, S.113, T.115 Chain C: H.95, N.96 Chain D: E.57, N.58 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.115, B:T.115, B:D.111, B:G.112, B:H.33, B:S.52, B:S.52, B:D.111, B:T.115 Hydrophobic interactions: B:R.110

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.2: 7 residues within 4Å: Chain D: N.107 Chain E: D.56, N.58, F.114, T.115 Chain F: D.89, T.94 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.56, E:N.58, E:T.115 NAG-NAG-BMA.13: 4 residues within 4Å: Chain D: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 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.3: 5 residues within 4Å: Chain D: T.105, N.118, S.120, Y.135, D.290 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 3 residues within 4Å: Chain D: T.98, Q.100, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain D: V.144, R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain D: N.265, N.301, S.303, S.381, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain D: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain D: N.332, S.333, S.334, S.357 Ligands: NAG-NAG.11, NAG-NAG.11, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG-NAG.10, NAG-NAG.10, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain D: N.361 Ligands: NAG-NAG.10, NAG-NAG.11 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.6: 13 residues within 4Å: Chain D: S.179, E.181, P.182, L.231, N.232, R.274, N.346, C.347, G.348, C.413, V.414, S.415 Ligands: NAG-NAG-BMA.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.181

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.9: 16 residues within 4Å: Chain D: R.296, H.299, N.301, T.383, R.412 Chain E: R.103, I.104, G.106, V.107, V.108 Chain F: N.44, N.45, N.46, P.60, G.61, S.62 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:R.296, E:V.107 Hydrophobic interactions: E:V.108

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.14: 4 residues within 4Å: Chain A: R.74, R.77 Chain D: K.458, E.460 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Salt bridges: D:K.458, A:R.74, A:R.77 SO4.18: 5 residues within 4Å: Chain D: T.248, N.250, G.426, G.427, N.430 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.250 SO4.19: 2 residues within 4Å: Chain D: K.197, K.453 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:K.197, D:K.201, D:K.453 SO4.20: 1 residues within 4Å: Chain D: R.128 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.128 SO4.28: 2 residues within 4Å: Chain F: D.152, S.153 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.153 Salt bridges: F:K.190

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

NAG.15: 2 residues within 4Å: Chain A: N.100, S.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.100, A:S.102 NAG.16: 4 residues within 4Å: Chain A: N.107 Chain C: E.55, R.56 Chain D: E.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.107, C:R.56 NAG.17: 2 residues within 4Å: Chain A: E.123, N.126 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain D: T.102, N.103 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.103 NAG.22: 4 residues within 4Å: Chain D: N.204, T.206, S.244, I.247 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.204, D:T.206, D:T.206 NAG.23: 3 residues within 4Å: Chain D: N.246, T.248, N.249 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.248, D:N.249 NAG.24: 1 residues within 4Å: Chain D: N.324 No protein-ligand interaction detected (PLIP) NAG.25: 2 residues within 4Å: Chain D: N.308, W.364 No protein-ligand interaction detected (PLIP) NAG.27: 3 residues within 4Å: Chain E: S.7, T.21, N.23 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.21 Hydrogen bonds: E:S.7

1 x 83G: 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione(Non-covalent)

83G.26: 16 residues within 4Å: Chain D: I.79, W.82, D.83, L.86, V.225, E.339, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, M.402, M.443 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.82, D:W.82, D:F.351, D:I.392, D:M.394, D:W.395, D:M.402 Hydrogen bonds: D:D.83, D:W.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pancera, M. et al., Crystal structures of trimeric HIV envelope with entry inhibitors BMS-378806 and BMS-626529. Nat. Chem. Biol. (2017)

Release Date

2017-08-30

Peptides

Envelope glycoprotein gp160: A
35O22 FAB HEAVY CHAIN: B
35O22 FAB LIGHT CHAIN: C
Envelope glycoprotein gp160: D
PGT122 FAB HEAVY CHAIN: E
PGT122 FAB LIGHT CHAIN: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

D
G

E
H

F
L

Envelope glycoprotein gp160

35O22 FAB HEAVY CHAIN

35O22 FAB LIGHT CHAIN

Envelope glycoprotein gp160

PGT122 FAB HEAVY CHAIN

PGT122 FAB LIGHT CHAIN

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