- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-3-1-1-3-mer
- Ligands
- 2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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.1: 17 residues within 4Å:- Chain A: Q.100, N.122, K.133
- Chain D: T.31, Y.32, H.53, E.54, S.100, K.101, H.102, R.103, L.104
- Chain E: H.31, G.32, D.33, R.34, N.35
8 PLIP interactions:2 interactions with chain D, 6 interactions with chain E- Hydrogen bonds: D:R.103, D:R.103, E:H.31, E:G.32, E:G.32, E:R.34, E:N.35, E:N.35
NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.10: 11 residues within 4Å:- Chain C: T.98, Q.100, S.120, N.122
- Chain D: G.55, D.56, K.57, K.58, K.65, W.72, R.74
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:G.55
- 18 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG-NAG.2: 3 residues within 4Å:- Chain A: N.265, N.301, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.3: 4 residues within 4Å:- Chain A: N.355
- Ligands: NAG-NAG.4, NAG-NAG.4, NAG.33
No protein-ligand interaction detected (PLIP)NAG-NAG.4: 6 residues within 4Å:- Chain A: N.332, S.333, T.341, S.357
- Ligands: NAG-NAG.3, NAG-NAG.3
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 3 residues within 4Å:- Chain A: N.118, Y.135, D.290
No protein-ligand interaction detected (PLIP)NAG-NAG.7: 3 residues within 4Å:- Chain B: N.106, N.118, Y.135
No protein-ligand interaction detected (PLIP)NAG-NAG.9: 4 residues within 4Å:- Chain C: T.267, H.299, N.301, T.383
No protein-ligand interaction detected (PLIP)NAG-NAG.11: 5 residues within 4Å:- Chain C: N.355, S.357
- Ligands: NAG-NAG.12, NAG-NAG.12, NAG.51
No protein-ligand interaction detected (PLIP)NAG-NAG.12: 5 residues within 4Å:- Chain C: N.332, T.341, N.355
- Ligands: NAG-NAG.11, NAG-NAG.11
No protein-ligand interaction detected (PLIP)NAG-NAG.13: 4 residues within 4Å:- Chain C: V.144, R.162, N.167, T.168
No protein-ligand interaction detected (PLIP)NAG-NAG.14: 3 residues within 4Å:- Chain A: R.162, N.167
- Chain C: R.278
No protein-ligand interaction detected (PLIP)NAG-NAG.18: 2 residues within 4Å:- Chain C: N.246, T.248
No protein-ligand interaction detected (PLIP)NAG-NAG.19: 4 residues within 4Å:- Chain C: Q.263, N.265, R.412, V.414
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:Q.263
NAG-NAG.20: 3 residues within 4Å:- Chain A: R.278
- Chain B: R.162, N.167
No protein-ligand interaction detected (PLIP)NAG-NAG.21: 3 residues within 4Å:- Chain B: N.246, T.248, N.249
No protein-ligand interaction detected (PLIP)NAG-NAG.22: 3 residues within 4Å:- Chain B: Q.263, N.265, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.23: 5 residues within 4Å:- Chain B: N.332, S.333, T.341
- Ligands: NAG-NAG.24, NAG-NAG.24
No protein-ligand interaction detected (PLIP)NAG-NAG.24: 5 residues within 4Å:- Chain B: N.355, S.357
- Ligands: NAG-NAG.23, NAG-NAG.23, NAG.42
No protein-ligand interaction detected (PLIP)NAG-NAG.25: 5 residues within 4Å:- Chain B: N.232, P.261, V.414, N.416
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN.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-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN-MAN-MAN.6: 14 residues within 4Å:- Chain B: T.98, Q.100, S.120, F.121, N.122
- Chain D: D.106, Y.107, V.120, V.122, Y.124
- Chain E: H.31, G.32, R.97, E.98
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:Q.100, B:Q.100
- Hydrophobic interactions: D:V.120
- 3 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.8: 8 residues within 4Å:- Chain B: E.181, L.231, N.232, N.346, G.348, V.414, S.415
- Ligands: NAG-NAG.25
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:G.348
NAG-NAG-BMA-MAN-MAN-MAN.15: 8 residues within 4Å:- Chain A: E.181, V.224, L.231, N.232, N.346, V.414, S.415
- Ligands: NAG.34
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:V.414
NAG-NAG-BMA-MAN-MAN-MAN.17: 8 residues within 4Å:- Chain C: K.35, E.181, L.231, N.232, G.348, V.414, S.415
- Ligands: NAG.52
No protein-ligand interaction detected (PLIP)- 1 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.16: 3 residues within 4Å:- Chain A: N.246, T.248, N.249
No protein-ligand interaction detected (PLIP)- 33 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.26: 4 residues within 4Å:- Chain A: E.57, N.58
- Chain F: G.16, S.17
Ligand excluded by PLIPNAG.27: 1 residues within 4Å:- Chain A: N.103
Ligand excluded by PLIPNAG.28: 3 residues within 4Å:- Chain A: N.204, T.206, S.244
Ligand excluded by PLIPNAG.29: 3 residues within 4Å:- Chain A: N.271, I.292, V.410
Ligand excluded by PLIPNAG.30: 5 residues within 4Å:- Chain A: T.267, H.299, N.301, S.381, T.383
Ligand excluded by PLIPNAG.31: 2 residues within 4Å:- Chain A: N.308, W.364
Ligand excluded by PLIPNAG.32: 1 residues within 4Å:- Chain A: N.324
Ligand excluded by PLIPNAG.33: 3 residues within 4Å:- Chain A: N.361
- Ligands: NAG-NAG.3, NAG-NAG.3
Ligand excluded by PLIPNAG.34: 4 residues within 4Å:- Chain A: P.261, V.414, N.416
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN.15
Ligand excluded by PLIPNAG.35: 4 residues within 4Å:- Chain B: E.57, N.58
- Chain G: G.16, S.17
Ligand excluded by PLIPNAG.36: 3 residues within 4Å:- Chain B: N.103, G.114, K.117
Ligand excluded by PLIPNAG.37: 3 residues within 4Å:- Chain B: N.204, T.206, S.244
Ligand excluded by PLIPNAG.38: 3 residues within 4Å:- Chain B: N.271, I.292, V.410
Ligand excluded by PLIPNAG.39: 4 residues within 4Å:- Chain B: N.265, T.267, H.299, N.301
Ligand excluded by PLIPNAG.40: 2 residues within 4Å:- Chain B: N.308, W.364
Ligand excluded by PLIPNAG.41: 1 residues within 4Å:- Chain B: N.324
Ligand excluded by PLIPNAG.42: 3 residues within 4Å:- Chain B: N.361
- Ligands: NAG-NAG.24, NAG-NAG.24
Ligand excluded by PLIPNAG.43: 1 residues within 4Å:- Chain B: N.107
Ligand excluded by PLIPNAG.44: 2 residues within 4Å:- Chain C: E.57, N.58
Ligand excluded by PLIPNAG.45: 2 residues within 4Å:- Chain C: N.103, K.117
Ligand excluded by PLIPNAG.46: 3 residues within 4Å:- Chain C: V.104, N.118, Y.135
Ligand excluded by PLIPNAG.47: 4 residues within 4Å:- Chain C: N.204, T.206, S.244, E.245
Ligand excluded by PLIPNAG.48: 3 residues within 4Å:- Chain C: N.271, I.292, V.410
Ligand excluded by PLIPNAG.49: 3 residues within 4Å:- Chain C: K.304, N.308, W.364
Ligand excluded by PLIPNAG.50: 2 residues within 4Å:- Chain C: K.320, N.324
Ligand excluded by PLIPNAG.51: 3 residues within 4Å:- Chain C: N.361
- Ligands: NAG-NAG.11, NAG-NAG.11
Ligand excluded by PLIPNAG.52: 4 residues within 4Å:- Chain C: P.261, V.414, N.416
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN.17
Ligand excluded by PLIPNAG.53: 2 residues within 4Å:- Chain F: N.100, S.102
Ligand excluded by PLIPNAG.54: 1 residues within 4Å:- Chain F: N.126
Ligand excluded by PLIPNAG.55: 2 residues within 4Å:- Chain G: N.100, S.102
Ligand excluded by PLIPNAG.56: 2 residues within 4Å:- Chain G: E.123, N.126
Ligand excluded by PLIPNAG.57: 2 residues within 4Å:- Chain H: N.100, S.102
Ligand excluded by PLIPNAG.58: 1 residues within 4Å:- Chain H: N.126
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kanai, T. et al., Structural Development of the HIV-1 Apex-Directed PGT145-PGDM1400 Antibody Lineage. Cell Rep (2024)
- Release Date
- 2024-12-25
- Peptides
- HIV-1 BG505 DS-SOSIP gp120: ABC
PGDM1400 heavy chain: D
PGDM1400 light chain: E
HIV-1 BG505 DS-SOSIP glycoprotein gp41: FGH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
HE
LF
aG
bH
c
SMTL ID : 9d1w.1
Cryo-EM structure of PGDM1400 Fab bound to HIV-1 BG505 DS-SOSIP.664 Env trimer
HIV-1 BG505 DS-SOSIP gp120
Toggle Identical (BC)PGDM1400 heavy chain
PGDM1400 light chain
HIV-1 BG505 DS-SOSIP glycoprotein gp41
Toggle Identical (FG)Related Entries With Identical Sequence
4rqq.1 | 4rqq.2 | 4rqq.3 | 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 more...less...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 | 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 | 9d3d.1