SMTL ID : 6mtn.1

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor Compound 484 in Complex with Human Antibodies 3H109L and 35O22 at 3.0 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

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

Ligands

4 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: 2 residues within 4Å: Chain B: N.69, E.90 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain D: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain D: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.2: 20 residues within 4Å: Chain A: L.9, G.16, S.17 Chain B: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, R.110, D.111, G.112, S.113, T.115 Chain C: H.96, N.97 Chain D: E.57, N.58 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.115 Hydrogen bonds: B:H.33, B:S.52, B:T.115, B:G.112, B:T.115, B:T.115, B:D.111, B:S.113

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.3: 6 residues within 4Å: Chain D: V.104, N.118, S.120, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 10 residues within 4Å: Chain D: E.181, L.231, N.232, N.346, G.348, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP)

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-(1-6)-[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-MAN-MAN-MAN.7: 21 residues within 4Å: Chain D: T.267, R.296, H.299, N.301, R.412 Chain E: Q.100, G.101, K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain F: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.296, D:R.296, E:V.108, E:R.103

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

NAG.9: 2 residues within 4Å: Chain A: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG.10: 10 residues within 4Å: Chain A: R.106, E.110, N.114, M.115, Q.119 Chain B: Q.1, Y.32, L.108, L.109 Chain C: P.59 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.106, A:R.106, A:N.114, B:Q.1 Hydrophobic interactions: B:L.108, B:L.109 NAG.11: 6 residues within 4Å: Chain D: C.101, T.102, N.103, D.110, D.111, R.113 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.103 NAG.12: 4 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Q.100 Hydrogen bonds: D:N.122 NAG.13: 2 residues within 4Å: Chain D: R.162, N.167 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.162, D:R.162, D:N.167 NAG.14: 4 residues within 4Å: Chain D: N.204, T.206, S.244, E.245 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.204 NAG.15: 3 residues within 4Å: Chain D: N.246, T.248, N.249 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.246, D:T.248 NAG.16: 1 residues within 4Å: Chain D: N.324 No protein-ligand interaction detected (PLIP) NAG.17: 5 residues within 4Å: Chain D: N.332, S.333, N.355, S.357 Ligands: NAG.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.332 NAG.18: 4 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG.17, NAG.19 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.357 NAG.19: 3 residues within 4Å: Chain D: G.358, N.361 Ligands: NAG.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.361

1 x JYJ: {4-[1-(3-chlorophenyl)cyclopropane-1-carbonyl]piperazin-1-yl}(thiophen-3-yl)methanone(Non-covalent)

JYJ.20: 17 residues within 4Å: Chain D: I.79, W.82, D.83, L.86, V.225, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, Q.400, A.401, M.402, M.443 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.79, D:W.82, D:L.86, D:V.225, D:M.394 Hydrogen bonds: D:W.395 pi-Stacking: D:F.351 Halogen bonds: D:I.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lai, Y.T. et al., Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry. Nat Commun (2019)

Release Date

2019-01-16

Peptides

Envelope glycoprotein gp160: A
35O22 scFv heavy chain portion: B
35O22 scFv light chain portion: C
Envelope glycoprotein gp160: D
3H109L Fab heavy chain: E
3H109L 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 scFv heavy chain portion

35O22 scFv light chain portion

Envelope glycoprotein gp160

3H109L Fab heavy chain

3H109L Fab light chain

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