- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.99 Å
- Oligo State
- hetero-3-3-3-3-3-3-mer
- Ligands
- 3 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
- 6 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: 4 residues within 4Å:- Chain D: V.104, N.118, Y.135, D.290
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.3: 11 residues within 4Å:- Chain D: E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415
- Ligands: NAG-NAG.7
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:G.348
NAG-NAG-BMA.21: 4 residues within 4Å:- Chain H: V.104, N.118, Y.135, D.290
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.22: 11 residues within 4Å:- Chain H: E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415
- Ligands: NAG-NAG.26
1 PLIP interactions:1 interactions with chain H- Hydrogen bonds: H:G.348
NAG-NAG-BMA.40: 4 residues within 4Å:- Chain L: V.104, N.118, Y.135, D.290
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.41: 11 residues within 4Å:- Chain L: E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415
- Ligands: NAG-NAG.45
1 PLIP interactions:1 interactions with chain L- Hydrogen bonds: L:G.348
- 9 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: 4 residues within 4Å:- Chain D: Q.263, N.265, S.303, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 3 residues within 4Å:- Chain D: N.271, I.292, V.410
No protein-ligand interaction detected (PLIP)NAG-NAG.7: 4 residues within 4Å:- Chain D: N.232, P.261, N.416
- Ligands: NAG-NAG-BMA.3
No protein-ligand interaction detected (PLIP)NAG-NAG.23: 4 residues within 4Å:- Chain H: Q.263, N.265, S.303, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.24: 3 residues within 4Å:- Chain H: N.271, I.292, V.410
No protein-ligand interaction detected (PLIP)NAG-NAG.26: 4 residues within 4Å:- Chain H: N.232, P.261, N.416
- Ligands: NAG-NAG-BMA.22
No protein-ligand interaction detected (PLIP)NAG-NAG.42: 4 residues within 4Å:- Chain L: Q.263, N.265, S.303, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.43: 3 residues within 4Å:- Chain L: N.271, I.292, V.410
No protein-ligand interaction detected (PLIP)NAG-NAG.45: 4 residues within 4Å:- Chain L: N.232, P.261, N.416
- Ligands: NAG-NAG-BMA.41
No protein-ligand interaction detected (PLIP)- 3 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.6: 6 residues within 4Å:- Chain D: T.267, R.296, H.299, N.301, T.383, R.412
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:R.296
NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.25: 6 residues within 4Å:- Chain H: T.267, R.296, H.299, N.301, T.383, R.412
1 PLIP interactions:1 interactions with chain H- Hydrogen bonds: H:R.296
NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.44: 6 residues within 4Å:- Chain L: T.267, R.296, H.299, N.301, T.383, R.412
1 PLIP interactions:1 interactions with chain L- Hydrogen bonds: L:R.296
- 33 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.8: 2 residues within 4Å:- Chain A: N.100, S.102
Ligand excluded by PLIPNAG.9: 3 residues within 4Å:- Chain A: E.123, N.126, Y.127
Ligand excluded by PLIPNAG.10: 1 residues within 4Å:- Chain B: N.69
Ligand excluded by PLIPNAG.11: 7 residues within 4Å:- Chain D: T.102, N.103, N.106, D.110, D.111, R.113, K.117
Ligand excluded by PLIPNAG.12: 5 residues within 4Å:- Chain D: Q.100, S.120, F.121, N.122, K.133
Ligand excluded by PLIPNAG.13: 4 residues within 4Å:- Chain D: R.162, N.167, T.168
- Chain L: R.278
Ligand excluded by PLIPNAG.14: 5 residues within 4Å:- Chain D: N.204, T.206, S.244, E.245, I.247
Ligand excluded by PLIPNAG.15: 3 residues within 4Å:- Chain D: N.246, T.248, N.249
Ligand excluded by PLIPNAG.16: 1 residues within 4Å:- Chain D: N.324
Ligand excluded by PLIPNAG.17: 5 residues within 4Å:- Chain D: N.332, S.333, N.355, S.357
- Ligands: NAG.18
Ligand excluded by PLIPNAG.18: 3 residues within 4Å:- Chain D: N.355, S.357
- Ligands: NAG.17
Ligand excluded by PLIPNAG.27: 2 residues within 4Å:- Chain E: N.100, S.102
Ligand excluded by PLIPNAG.28: 3 residues within 4Å:- Chain E: E.123, N.126, Y.127
Ligand excluded by PLIPNAG.29: 1 residues within 4Å:- Chain F: N.69
Ligand excluded by PLIPNAG.30: 7 residues within 4Å:- Chain H: T.102, N.103, N.106, D.110, D.111, R.113, K.117
Ligand excluded by PLIPNAG.31: 5 residues within 4Å:- Chain H: Q.100, S.120, F.121, N.122, K.133
Ligand excluded by PLIPNAG.32: 4 residues within 4Å:- Chain D: R.278
- Chain H: R.162, N.167, T.168
Ligand excluded by PLIPNAG.33: 5 residues within 4Å:- Chain H: N.204, T.206, S.244, E.245, I.247
Ligand excluded by PLIPNAG.34: 3 residues within 4Å:- Chain H: N.246, T.248, N.249
Ligand excluded by PLIPNAG.35: 1 residues within 4Å:- Chain H: N.324
Ligand excluded by PLIPNAG.36: 5 residues within 4Å:- Chain H: N.332, S.333, N.355, S.357
- Ligands: NAG.37
Ligand excluded by PLIPNAG.37: 3 residues within 4Å:- Chain H: N.355, S.357
- Ligands: NAG.36
Ligand excluded by PLIPNAG.46: 2 residues within 4Å:- Chain I: N.100, S.102
Ligand excluded by PLIPNAG.47: 3 residues within 4Å:- Chain I: E.123, N.126, Y.127
Ligand excluded by PLIPNAG.48: 1 residues within 4Å:- Chain J: N.69
Ligand excluded by PLIPNAG.49: 7 residues within 4Å:- Chain L: T.102, N.103, N.106, D.110, D.111, R.113, K.117
Ligand excluded by PLIPNAG.50: 5 residues within 4Å:- Chain L: Q.100, S.120, F.121, N.122, K.133
Ligand excluded by PLIPNAG.51: 4 residues within 4Å:- Chain H: R.278
- Chain L: R.162, N.167, T.168
Ligand excluded by PLIPNAG.52: 5 residues within 4Å:- Chain L: N.204, T.206, S.244, E.245, I.247
Ligand excluded by PLIPNAG.53: 3 residues within 4Å:- Chain L: N.246, T.248, N.249
Ligand excluded by PLIPNAG.54: 1 residues within 4Å:- Chain L: N.324
Ligand excluded by PLIPNAG.55: 5 residues within 4Å:- Chain L: N.332, S.333, N.355, S.357
- Ligands: NAG.56
Ligand excluded by PLIPNAG.56: 3 residues within 4Å:- Chain L: N.355, S.357
- Ligands: NAG.55
Ligand excluded by PLIP- 3 x JYS: 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-1,2-dione(Non-covalent)
JYS.19: 18 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, Q.400, A.401, M.402, M.443
14 PLIP interactions:14 interactions with chain D- Hydrophobic interactions: D:W.82, D:L.86, D:V.225, D:E.339, D:F.351, D:F.351, D:I.392, D:M.394, D:Q.400, D:M.402
- Hydrogen bonds: D:D.83, D:W.395
- pi-Stacking: D:W.395, D:W.395
JYS.38: 18 residues within 4Å:- Chain H: 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, Q.400, A.401, M.402, M.443
14 PLIP interactions:14 interactions with chain H- Hydrophobic interactions: H:W.82, H:L.86, H:V.225, H:E.339, H:F.351, H:F.351, H:I.392, H:M.394, H:Q.400, H:M.402
- Hydrogen bonds: H:D.83, H:W.395
- pi-Stacking: H:W.395, H:W.395
JYS.57: 18 residues within 4Å:- Chain L: 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, Q.400, A.401, M.402, M.443
14 PLIP interactions:14 interactions with chain L- Hydrophobic interactions: L:W.82, L:L.86, L:V.225, L:E.339, L:F.351, L:F.351, L:I.392, L:M.394, L:Q.400, L:M.402
- Hydrogen bonds: L:D.83, L:W.395
- pi-Stacking: L:W.395, L:W.395
- 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: AEI
35O22 scFv heavy chain portion: BFJ
35O22 scFv light chain portion: CGK
Envelope glycoprotein gp160: DHL
3H109L Fab heavy chain: MOQ
3H109L Fab light chain: NPR - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BE
BI
BB
DF
DJ
DC
EG
EK
ED
GH
GL
GM
HO
HQ
HN
LP
LR
L
SMTL ID : 6mu8.1
Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-386150 in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom
Envelope glycoprotein gp160
Toggle Identical (AEI)35O22 scFv heavy chain portion
Toggle Identical (BFJ)35O22 scFv light chain portion
Toggle Identical (CGK)Envelope glycoprotein gp160
Toggle Identical (DHL)3H109L Fab heavy chain
Toggle Identical (MOQ)3H109L Fab light chain
Toggle Identical (NPR)Related Entries With Identical Sequence
4tvp.1 | 4zmj.1 | 5aco.1 | 5c7k.1 | 5cez.2 | 5cjx.1 | 5fyl.1 | 5t3x.1 | 5t3z.1 | 5thr.1 | 5u7m.1 | 5u7o.1 | 5utf.1 | 5uty.1 | 5v7j.1 | 5v8l.1 | 5v8m.1 | 5viy.1 | 5vj6.1 | 5w6d.1 | 6ck9.1 | 6cm3.1 | 6crq.1 | 6de7.1 | 6did.1 | 6mn7.1 | 6mtj.1 | 6mtn.1 | 6mu6.1 | 6mu7.1 more...less...6muf.1 | 6mug.1 | 6nf2.1 | 6nm6.1 | 6nnf.1 | 6nnj.1 | 6opa.1 | 6osy.1 | 6ot1.1 | 6oz4.1 | 6ozc.1 | 6pw6.1 | 6u0l.1 | 6u0n.1 | 6udj.1 | 6vi0.1 | 6vn0.1 | 6vzi.1 | 6w03.1 | 6wix.1 | 6x96.1 | 6x97.1 | 6x98.1 | 6x9r.1 | 6x9r.2 | 6x9r.3 | 6x9s.1 | 6x9s.2 | 6x9s.3 | 6x9t.1 | 6x9t.2 | 6x9t.3 | 6x9u.1 | 6x9u.2 | 6x9u.3 | 6x9v.1 | 6x9v.2 | 6x9v.3 | 6xrt.1 | 7kde.1 | 7lo6.1 | 7lok.1 | 7lpn.1 | 7mxe.1 | 7pc2.1 | 7rai.1 | 7tfn.1 | 7tfo.1 | 7txd.1 | 7ucf.1 | 7uoj.1 | 8dp1.1 | 8dto.1 | 8e1p.1 | 8euu.1 | 8euv.1 | 8euw.1 | 8fis.1 | 8fk5.1 | 8fl1.1 | 8flw.1 | 8fyj.1 | 8g85.1 | 8g9w.1 | 8g9x.1 | 8g9y.1 | 8gas.1 | 8jtd.1 | 8jtm.1 | 8sal.1 | 8san.1 | 8saq.1 | 8sat.1 | 8sav.1 | 8sw3.1 | 8sw4.1 | 8tjr.1 | 8tjs.1 | 8tkc.1 | 8tl2.1 | 8tl3.1 | 8tl4.1 | 8tl5.1 | 8tng.1 | 8tnh.1 | 8tni.1 | 8tnu.1 | 8to7.1 | 8top.1 | 8tq1.1 | 8ttw.1