- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-3-3-1-1-mer
- Ligands
- 17 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: 4 residues within 4Å:- Chain C: Q.100, S.120, F.121, N.122
No protein-ligand interaction detected (PLIP)NAG-NAG.2: 3 residues within 4Å:- Chain C: V.144, R.162, N.167
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:V.144
NAG-NAG.4: 3 residues within 4Å:- Chain C: N.246, T.248, N.249
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 3 residues within 4Å:- Chain C: Q.263, N.265, S.303
No protein-ligand interaction detected (PLIP)NAG-NAG.6: 4 residues within 4Å:- Chain C: N.332, S.357
- Ligands: NAG-NAG.7, NAG-NAG.7
No protein-ligand interaction detected (PLIP)NAG-NAG.7: 5 residues within 4Å:- Chain C: N.355, S.357
- Ligands: NAG-NAG.6, NAG-NAG.6, NAG.37
No protein-ligand interaction detected (PLIP)NAG-NAG.8: 2 residues within 4Å:- Chain E: R.162, N.167
No protein-ligand interaction detected (PLIP)NAG-NAG.10: 3 residues within 4Å:- Chain E: Q.263, N.265, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.11: 6 residues within 4Å:- Chain E: N.332, S.333, T.341, N.355
- Ligands: NAG-NAG.12, NAG-NAG.12
No protein-ligand interaction detected (PLIP)NAG-NAG.12: 5 residues within 4Å:- Chain E: N.355, S.357
- Ligands: NAG-NAG.11, NAG-NAG.11, NAG.51
No protein-ligand interaction detected (PLIP)NAG-NAG.13: 4 residues within 4Å:- Chain E: N.232, P.261, N.416
- Ligands: NAG-NAG-BMA-MAN-MAN.9
No protein-ligand interaction detected (PLIP)NAG-NAG.15: 2 residues within 4Å:- Chain F: R.162, N.167
No protein-ligand interaction detected (PLIP)NAG-NAG.17: 3 residues within 4Å:- Chain F: N.246, T.248, N.249
No protein-ligand interaction detected (PLIP)NAG-NAG.18: 4 residues within 4Å:- Chain F: Q.263, N.265, S.303, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.19: 5 residues within 4Å:- Chain F: N.332, S.333, G.335
- Ligands: NAG-NAG.20, NAG-NAG.20
No protein-ligand interaction detected (PLIP)NAG-NAG.20: 4 residues within 4Å:- Chain F: N.355, S.357
- Ligands: NAG-NAG.19, NAG-NAG.19
No protein-ligand interaction detected (PLIP)NAG-NAG.21: 5 residues within 4Å:- Chain F: N.232, L.235, P.261, N.416
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN.16
No protein-ligand interaction detected (PLIP)- 2 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.3: 10 residues within 4Å:- Chain C: K.35, E.181, L.231, N.232, N.346, G.348, C.413, V.414, S.415
- Ligands: NAG.38
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:G.348, C:V.414
NAG-NAG-BMA-MAN-MAN-MAN.16: 10 residues within 4Å:- Chain F: E.181, P.182, V.224, L.231, N.232, G.348, C.413, V.414, S.415
- Ligands: NAG-NAG.21
2 PLIP interactions:2 interactions with chain F- Hydrophobic interactions: F:V.414
- Hydrogen bonds: F:V.414
- 1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.9: 11 residues within 4Å:- Chain E: S.179, P.182, N.232, N.346, G.348, Q.408, R.412, C.413, V.414, S.415
- Ligands: NAG-NAG.13
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:V.414, E:Q.408
- 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.14: 7 residues within 4Å:- Chain E: T.98, Q.100, N.122, K.133
- Chain G: G.100, Y.120, Y.122
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA-MAN-MAN.22: 8 residues within 4Å:- Chain F: V.104, N.106, N.118, Y.135, L.137, D.290
- Chain G: D.53, F.113
1 PLIP interactions:1 interactions with chain G- Hydrophobic interactions: G:F.113
- 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.23: 13 residues within 4Å:- Chain F: T.98, Q.100, S.120, F.121, N.122
- Chain G: D.103, R.105, Y.110, Y.118, N.119, Y.120, H.121
- Chain H: D.52
2 PLIP interactions:2 interactions with chain G- Hydrophobic interactions: G:Y.118
- Hydrogen bonds: G:D.103
- 40 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.24: 2 residues within 4Å:- Chain A: N.100, S.102
Ligand excluded by PLIPNAG.25: 1 residues within 4Å:- Chain A: N.126
Ligand excluded by PLIPNAG.26: 1 residues within 4Å:- Chain A: N.107
Ligand excluded by PLIPNAG.27: 2 residues within 4Å:- Chain B: N.100, S.102
Ligand excluded by PLIPNAG.28: 1 residues within 4Å:- Chain B: N.126
Ligand excluded by PLIPNAG.29: 2 residues within 4Å:- Chain C: E.57, N.58
Ligand excluded by PLIPNAG.30: 2 residues within 4Å:- Chain C: N.103, K.117
Ligand excluded by PLIPNAG.31: 5 residues within 4Å:- Chain C: V.104, N.106, N.118, L.137, D.290
Ligand excluded by PLIPNAG.32: 4 residues within 4Å:- Chain C: N.204, T.206, S.244, H.321
Ligand excluded by PLIPNAG.33: 2 residues within 4Å:- Chain C: N.271, I.292
Ligand excluded by PLIPNAG.34: 4 residues within 4Å:- Chain C: T.267, H.299, N.301, R.412
Ligand excluded by PLIPNAG.35: 1 residues within 4Å:- Chain C: N.308
Ligand excluded by PLIPNAG.36: 1 residues within 4Å:- Chain C: N.324
Ligand excluded by PLIPNAG.37: 3 residues within 4Å:- Chain C: N.361
- Ligands: NAG-NAG.7, NAG-NAG.7
Ligand excluded by PLIPNAG.38: 4 residues within 4Å:- Chain C: N.232, P.261, N.416
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN.3
Ligand excluded by PLIPNAG.39: 2 residues within 4Å:- Chain C: N.106, N.107
Ligand excluded by PLIPNAG.40: 2 residues within 4Å:- Chain D: N.100, S.102
Ligand excluded by PLIPNAG.41: 1 residues within 4Å:- Chain D: N.126
Ligand excluded by PLIPNAG.42: 2 residues within 4Å:- Chain D: N.105, N.107
Ligand excluded by PLIPNAG.43: 2 residues within 4Å:- Chain B: S.17
- Chain E: N.58
Ligand excluded by PLIPNAG.44: 2 residues within 4Å:- Chain E: N.103, K.117
Ligand excluded by PLIPNAG.45: 4 residues within 4Å:- Chain E: V.104, N.118, L.137, D.290
Ligand excluded by PLIPNAG.46: 3 residues within 4Å:- Chain E: N.204, T.206, S.244
Ligand excluded by PLIPNAG.47: 3 residues within 4Å:- Chain E: N.271, I.292, V.410
Ligand excluded by PLIPNAG.48: 4 residues within 4Å:- Chain E: T.267, H.299, N.301, T.383
Ligand excluded by PLIPNAG.49: 2 residues within 4Å:- Chain E: K.304, N.308
Ligand excluded by PLIPNAG.50: 1 residues within 4Å:- Chain E: N.324
Ligand excluded by PLIPNAG.51: 3 residues within 4Å:- Chain E: N.361
- Ligands: NAG-NAG.12, NAG-NAG.12
Ligand excluded by PLIPNAG.52: 4 residues within 4Å:- Chain E: N.106, N.107, G.293, D.294
Ligand excluded by PLIPNAG.53: 3 residues within 4Å:- Chain E: N.246, T.248, N.249
Ligand excluded by PLIPNAG.54: 2 residues within 4Å:- Chain F: E.57, N.58
Ligand excluded by PLIPNAG.55: 2 residues within 4Å:- Chain F: N.103, G.114
Ligand excluded by PLIPNAG.56: 3 residues within 4Å:- Chain F: N.204, S.244, I.247
Ligand excluded by PLIPNAG.57: 2 residues within 4Å:- Chain F: N.271, I.292
Ligand excluded by PLIPNAG.58: 5 residues within 4Å:- Chain F: T.267, H.299, N.301, T.383, R.412
Ligand excluded by PLIPNAG.59: 2 residues within 4Å:- Chain F: K.304, N.308
Ligand excluded by PLIPNAG.60: 1 residues within 4Å:- Chain F: N.324
Ligand excluded by PLIPNAG.61: 1 residues within 4Å:- Chain F: N.361
Ligand excluded by PLIPNAG.62: 3 residues within 4Å:- Chain F: N.106, N.107, D.294
Ligand excluded by PLIPNAG.63: 1 residues within 4Å:- Chain F: N.430
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Holt, G.T. et al., Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design. Cell Rep (2023)
- Release Date
- 2023-05-31
- Peptides
- Envelope glycoprotein gp41: ABD
Envelope glycoprotein gp120: CEF
PG9 DU025 Heavy: G
PG9 DU025 Light: H - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BD
FC
CE
GF
IG
HH
L
SMTL ID : 8fl1.1
Cryo-EM Structure of PG9RSH DU025 Fab in complex with BG505 DS-SOSIP.664
Envelope glycoprotein gp41
Envelope glycoprotein gp120
PG9 DU025 Heavy
PG9 DU025 Light
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 | 6cm3.1 | 6crq.1 | 6de7.1 | 6did.1 | 6mn7.1 | 6mtj.1 | 6mtn.1 | 6mu6.1 | 6mu7.1 | 6mu8.1 more...less...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 | 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 | 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