- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-3-3-3-3-mer
- Ligands
- 2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 17 residues within 4Å:- Chain A: V.178, S.179, K.222, V.224, L.231, N.232, F.345, N.346, G.348, I.407, G.409, V.410, R.412, C.413, V.414, S.415
- Ligands: NAG-NAG.3
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.412
NAG-NAG-BMA-MAN-MAN-MAN-MAN.16: 17 residues within 4Å:- Chain E: V.178, S.179, F.180, E.181, P.182, K.222, L.231, N.232, N.346, G.348, I.407, G.409, V.410, R.412, C.413, V.414
- Ligands: NAG-NAG.18
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:G.348
- 8 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: 6 residues within 4Å:- Chain A: N.355, S.357
- Ligands: NAG-NAG-BMA.4, NAG-NAG-BMA.4, NAG-NAG-BMA.4, NAG-NAG.5
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.4: 8 residues within 4Å:- Chain A: N.332, S.333, T.341, N.355, S.357
- Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2, NAG-NAG-BMA.2
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.8: 3 residues within 4Å:- Chain A: N.246, T.248, N.249
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.13: 4 residues within 4Å:- Chain C: N.246, I.247, T.248, N.249
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.14: 7 residues within 4Å:- Chain C: N.332, S.333, T.341, N.355, S.357
- Ligands: NAG-NAG.11, NAG-NAG.11
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.17: 6 residues within 4Å:- Chain E: N.355, S.357
- Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.20, NAG-NAG-BMA.20, NAG-NAG.21
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.19: 3 residues within 4Å:- Chain E: N.246, T.248, N.249
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.20: 7 residues within 4Å:- Chain E: N.332, S.333, T.341, N.355
- Ligands: NAG-NAG-BMA.17, NAG-NAG-BMA.17, NAG-NAG-BMA.17
No protein-ligand interaction detected (PLIP)- 11 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG-NAG.3: 4 residues within 4Å:- Chain A: P.261, V.414, N.416
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 3 residues within 4Å:- Chain A: G.358, N.361
- Ligands: NAG-NAG-BMA.2
No protein-ligand interaction detected (PLIP)NAG-NAG.6: 4 residues within 4Å:- Chain A: N.204, T.206, G.207, H.321
No protein-ligand interaction detected (PLIP)NAG-NAG.7: 2 residues within 4Å:- Chain A: K.320, N.324
No protein-ligand interaction detected (PLIP)NAG-NAG.9: 1 residues within 4Å:- Chain B: N.100
No protein-ligand interaction detected (PLIP)NAG-NAG.11: 5 residues within 4Å:- Chain C: N.355, S.357
- Ligands: NAG-NAG-BMA.14, NAG-NAG-BMA.14, NAG-NAG-BMA.14
No protein-ligand interaction detected (PLIP)NAG-NAG.12: 5 residues within 4Å:- Chain C: P.261, V.414, S.415, N.416
- Ligands: NAG-NAG-BMA-MAN-MAN.10
No protein-ligand interaction detected (PLIP)NAG-NAG.15: 2 residues within 4Å:- Chain C: N.204, T.206
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:T.206
NAG-NAG.18: 3 residues within 4Å:- Chain E: V.414, N.416
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.16
No protein-ligand interaction detected (PLIP)NAG-NAG.21: 2 residues within 4Å:- Chain E: N.361
- Ligands: NAG-NAG-BMA.17
No protein-ligand interaction detected (PLIP)NAG-NAG.22: 2 residues within 4Å:- Chain F: N.100, S.102
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.10: 15 residues within 4Å:- Chain C: S.179, E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, I.407, R.412, C.413, V.414, S.415
- Ligands: NAG-NAG.12
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:E.181, C:G.348
- 30 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.23: 2 residues within 4Å:- Chain A: E.57, N.58
Ligand excluded by PLIPNAG.24: 4 residues within 4Å:- Chain A: N.265, S.303, S.381, R.412
Ligand excluded by PLIPNAG.25: 2 residues within 4Å:- Chain A: K.304, N.308
Ligand excluded by PLIPNAG.26: 4 residues within 4Å:- Chain A: H.299, N.301, S.381, T.383
Ligand excluded by PLIPNAG.27: 2 residues within 4Å:- Chain A: N.271, N.272
Ligand excluded by PLIPNAG.28: 1 residues within 4Å:- Chain A: N.430
Ligand excluded by PLIPNAG.29: 2 residues within 4Å:- Chain B: N.126, Y.127
Ligand excluded by PLIPNAG.30: 1 residues within 4Å:- Chain B: N.107
Ligand excluded by PLIPNAG.31: 1 residues within 4Å:- Chain B: N.114
Ligand excluded by PLIPNAG.32: 2 residues within 4Å:- Chain C: G.323, N.324
Ligand excluded by PLIPNAG.33: 5 residues within 4Å:- Chain C: N.308, E.309, S.362, W.364, T.368
Ligand excluded by PLIPNAG.34: 1 residues within 4Å:- Chain C: N.58
Ligand excluded by PLIPNAG.35: 4 residues within 4Å:- Chain C: N.265, S.303, S.381, R.412
Ligand excluded by PLIPNAG.36: 3 residues within 4Å:- Chain C: T.267, H.299, N.301
Ligand excluded by PLIPNAG.37: 1 residues within 4Å:- Chain C: N.361
Ligand excluded by PLIPNAG.38: 1 residues within 4Å:- Chain C: N.271
Ligand excluded by PLIPNAG.39: 2 residues within 4Å:- Chain D: E.123, N.126
Ligand excluded by PLIPNAG.40: 1 residues within 4Å:- Chain D: N.100
Ligand excluded by PLIPNAG.41: 1 residues within 4Å:- Chain D: N.107
Ligand excluded by PLIPNAG.42: 3 residues within 4Å:- Chain E: E.57, N.58
- Chain F: S.17
Ligand excluded by PLIPNAG.43: 3 residues within 4Å:- Chain E: H.299, N.301, S.381
Ligand excluded by PLIPNAG.44: 3 residues within 4Å:- Chain E: Q.263, N.265, R.412
Ligand excluded by PLIPNAG.45: 1 residues within 4Å:- Chain E: N.324
Ligand excluded by PLIPNAG.46: 1 residues within 4Å:- Chain E: N.430
Ligand excluded by PLIPNAG.47: 2 residues within 4Å:- Chain E: N.271, R.274
Ligand excluded by PLIPNAG.48: 2 residues within 4Å:- Chain E: N.204, S.244
Ligand excluded by PLIPNAG.49: 4 residues within 4Å:- Chain E: K.304, N.308, S.362, W.364
Ligand excluded by PLIPNAG.50: 2 residues within 4Å:- Chain F: N.107, S.109
Ligand excluded by PLIPNAG.51: 1 residues within 4Å:- Chain F: N.126
Ligand excluded by PLIPNAG.52: 1 residues within 4Å:- Chain F: N.114
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Glogl, M. et al., Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nat.Struct.Mol.Biol. (2023)
- Release Date
- 2023-04-12
- Peptides
- Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
T-cell surface glycoprotein CD4: GHI
Broadly neutralizing darpin bnd.9: JKL - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CE
EB
BD
DF
FG
GH
HI
IJ
JK
KL
L
SMTL ID : 7txd.1
Cryo-EM structure of BG505 SOSIP HIV-1 Env trimer in complex with CD4 receptor (D1D2) and broadly neutralizing darpin bnD.9
Envelope glycoprotein gp120
Toggle Identical (ACE)Envelope glycoprotein gp41
T-cell surface glycoprotein CD4
Toggle Identical (GHI)Broadly neutralizing darpin bnd.9
Toggle Identical (JKL)Related Entries With Identical Sequence
1g9m.1 | 1g9n.1 | 1gc1.1 | 1rzj.1 | 1rzk.1 | 3j70.1 | 4h8w.1 | 4jm2.1 | 4rqs.1 | 4rqs.2 | 4tvp.1 | 4zmj.1 | 5a8h.1 | 5aco.1 | 5c7k.1 | 5cez.2 | 5cjx.1 | 5fyl.1 | 5i8h.1 | 5i8h.2 | 5t3x.1 | 5t3z.1 | 5thr.1 | 5u7m.1 | 5u7o.1 | 5utf.1 | 5uty.1 | 5v7j.1 | 5v8l.1 | 5v8m.1 more...less...5viy.1 | 5vj6.1 | 5vn3.1 | 5w6d.1 | 6cm3.1 | 6crq.1 | 6de7.1 | 6did.1 | 6edu.1 | 6mn7.1 | 6mtj.1 | 6mtn.1 | 6mu6.1 | 6mu7.1 | 6mu8.1 | 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 | 6w03.1 | 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 | 7sd3.1 | 7tfn.1 | 7tfo.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