- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.94 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 6 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.1: 9 residues within 4Å:- Chain A: N.82, N.628
- Chain B: F.50, G.51, W.52, G.76, R.120, N.137
- Ligands: NAG-NAG-FUC.15
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:W.52
- Hydrogen bonds: A:N.628, A:N.628
NAG-NAG-BMA-MAN-MAN.8: 8 residues within 4Å:- Chain A: L.256, N.257, F.369, N.370, C.437, K.438, S.439
- Ligands: NAG.50
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:K.438
- Hydrogen bonds: A:K.438
NAG-NAG-BMA-MAN-MAN.16: 9 residues within 4Å:- Chain D: N.82, N.628
- Chain E: F.50, G.51, W.52, G.76, R.120, N.137
- Ligands: NAG-NAG-FUC.30
3 PLIP interactions:1 interactions with chain E, 2 interactions with chain D- Hydrophobic interactions: E:W.52
- Hydrogen bonds: D:N.628, D:N.628
NAG-NAG-BMA-MAN-MAN.23: 8 residues within 4Å:- Chain D: L.256, N.257, F.369, N.370, C.437, K.438, S.439
- Ligands: NAG.57
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:K.438
- Hydrogen bonds: D:K.438
NAG-NAG-BMA-MAN-MAN.31: 9 residues within 4Å:- Chain G: N.82, N.628
- Chain H: F.50, G.51, W.52, G.76, R.120, N.137
- Ligands: NAG-NAG-FUC.45
3 PLIP interactions:1 interactions with chain H, 2 interactions with chain G- Hydrophobic interactions: H:W.52
- Hydrogen bonds: G:N.628, G:N.628
NAG-NAG-BMA-MAN-MAN.38: 8 residues within 4Å:- Chain G: L.256, N.257, F.369, N.370, C.437, K.438, S.439
- Ligands: NAG.64
2 PLIP interactions:2 interactions with chain G- Hydrophobic interactions: G:K.438
- Hydrogen bonds: G:K.438
- 33 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: 6 residues within 4Å:- Chain A: V.128, N.129, T.130, N.147, Y.164, L.166
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:Y.164
NAG-NAG.3: 3 residues within 4Å:- Chain A: S.149, F.150, N.151
No protein-ligand interaction detected (PLIP)NAG-NAG.4: 4 residues within 4Å:- Chain A: R.187, N.192, T.193
- Chain G: R.303
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 7 residues within 4Å:- Chain A: N.225, F.228, N.229, T.231, P.233, N.235
- Ligands: NAG-NAG.6
No protein-ligand interaction detected (PLIP)NAG-NAG.6: 6 residues within 4Å:- Chain A: N.229, T.231, P.233, S.269, L.272
- Ligands: NAG-NAG.5
No protein-ligand interaction detected (PLIP)NAG-NAG.7: 3 residues within 4Å:- Chain A: V.79, N.224, N.236
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:V.79
NAG-NAG.9: 3 residues within 4Å:- Chain A: N.271, T.273, N.274
No protein-ligand interaction detected (PLIP)NAG-NAG.11: 5 residues within 4Å:- Chain A: Y.324, N.326, D.405, I.406, T.407
No protein-ligand interaction detected (PLIP)NAG-NAG.12: 5 residues within 4Å:- Chain A: N.353, T.355, T.457
- Ligands: NAG-NAG.14, NAG-NAG.14
No protein-ligand interaction detected (PLIP)NAG-NAG.13: 4 residues within 4Å:- Chain A: T.365, T.366, N.379, S.381
No protein-ligand interaction detected (PLIP)NAG-NAG.14: 4 residues within 4Å:- Chain A: S.381, S.382, N.385
- Ligands: NAG-NAG.12
No protein-ligand interaction detected (PLIP)NAG-NAG.17: 6 residues within 4Å:- Chain D: V.128, N.129, T.130, N.147, Y.164, L.166
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:Y.164
NAG-NAG.18: 3 residues within 4Å:- Chain D: S.149, F.150, N.151
No protein-ligand interaction detected (PLIP)NAG-NAG.19: 4 residues within 4Å:- Chain A: R.303
- Chain D: R.187, N.192, T.193
No protein-ligand interaction detected (PLIP)NAG-NAG.20: 7 residues within 4Å:- Chain D: N.225, F.228, N.229, T.231, P.233, N.235
- Ligands: NAG-NAG.21
No protein-ligand interaction detected (PLIP)NAG-NAG.21: 6 residues within 4Å:- Chain D: N.229, T.231, P.233, S.269, L.272
- Ligands: NAG-NAG.20
No protein-ligand interaction detected (PLIP)NAG-NAG.22: 3 residues within 4Å:- Chain D: V.79, N.224, N.236
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:V.79
NAG-NAG.24: 3 residues within 4Å:- Chain D: N.271, T.273, N.274
No protein-ligand interaction detected (PLIP)NAG-NAG.26: 5 residues within 4Å:- Chain D: Y.324, N.326, D.405, I.406, T.407
No protein-ligand interaction detected (PLIP)NAG-NAG.27: 5 residues within 4Å:- Chain D: N.353, T.355, T.457
- Ligands: NAG-NAG.29, NAG-NAG.29
No protein-ligand interaction detected (PLIP)NAG-NAG.28: 4 residues within 4Å:- Chain D: T.365, T.366, N.379, S.381
No protein-ligand interaction detected (PLIP)NAG-NAG.29: 4 residues within 4Å:- Chain D: S.381, S.382, N.385
- Ligands: NAG-NAG.27
No protein-ligand interaction detected (PLIP)NAG-NAG.32: 6 residues within 4Å:- Chain G: V.128, N.129, T.130, N.147, Y.164, L.166
1 PLIP interactions:1 interactions with chain G- Hydrophobic interactions: G:Y.164
NAG-NAG.33: 3 residues within 4Å:- Chain G: S.149, F.150, N.151
No protein-ligand interaction detected (PLIP)NAG-NAG.34: 4 residues within 4Å:- Chain D: R.303
- Chain G: R.187, N.192, T.193
No protein-ligand interaction detected (PLIP)NAG-NAG.35: 7 residues within 4Å:- Chain G: N.225, F.228, N.229, T.231, P.233, N.235
- Ligands: NAG-NAG.36
No protein-ligand interaction detected (PLIP)NAG-NAG.36: 6 residues within 4Å:- Chain G: N.229, T.231, P.233, S.269, L.272
- Ligands: NAG-NAG.35
No protein-ligand interaction detected (PLIP)NAG-NAG.37: 3 residues within 4Å:- Chain G: V.79, N.224, N.236
1 PLIP interactions:1 interactions with chain G- Hydrophobic interactions: G:V.79
NAG-NAG.39: 3 residues within 4Å:- Chain G: N.271, T.273, N.274
No protein-ligand interaction detected (PLIP)NAG-NAG.41: 5 residues within 4Å:- Chain G: Y.324, N.326, D.405, I.406, T.407
No protein-ligand interaction detected (PLIP)NAG-NAG.42: 5 residues within 4Å:- Chain G: N.353, T.355, T.457
- Ligands: NAG-NAG.44, NAG-NAG.44
No protein-ligand interaction detected (PLIP)NAG-NAG.43: 4 residues within 4Å:- Chain G: T.365, T.366, N.379, S.381
No protein-ligand interaction detected (PLIP)NAG-NAG.44: 4 residues within 4Å:- Chain G: S.381, S.382, N.385
- Ligands: NAG-NAG.42
No protein-ligand interaction detected (PLIP)- 3 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.10: 7 residues within 4Å:- Chain A: G.263, E.264, I.265, N.284, E.285, R.338, K.341
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:K.341
NAG-NAG-BMA.25: 7 residues within 4Å:- Chain D: G.263, E.264, I.265, N.284, E.285, R.338, K.341
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:K.341
NAG-NAG-BMA.40: 7 residues within 4Å:- Chain G: G.263, E.264, I.265, N.284, E.285, R.338, K.341
1 PLIP interactions:1 interactions with chain G- Hydrophobic interactions: G:K.341
- 3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-FUC.15: 4 residues within 4Å:- Chain A: K.620, N.628
- Ligands: NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1
No protein-ligand interaction detected (PLIP)NAG-NAG-FUC.30: 4 residues within 4Å:- Chain D: K.620, N.628
- Ligands: NAG-NAG-BMA-MAN-MAN.16, NAG-NAG-BMA-MAN-MAN.16
No protein-ligand interaction detected (PLIP)NAG-NAG-FUC.45: 4 residues within 4Å:- Chain G: K.620, N.628
- Ligands: NAG-NAG-BMA-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN.31
No protein-ligand interaction detected (PLIP)- 21 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.46: 3 residues within 4Å:- Chain A: K.180, N.182, S.183
Ligand excluded by PLIPNAG.47: 5 residues within 4Å:- Chain A: N.296, I.317, G.433, N.434
- Ligands: NAG.49
Ligand excluded by PLIPNAG.48: 4 residues within 4Å:- Chain A: R.349, N.389, N.391, D.392
Ligand excluded by PLIPNAG.49: 2 residues within 4Å:- Chain A: N.434
- Ligands: NAG.47
Ligand excluded by PLIPNAG.50: 4 residues within 4Å:- Chain A: N.257, S.286, N.440
- Ligands: NAG-NAG-BMA-MAN-MAN.8
Ligand excluded by PLIPNAG.51: 3 residues within 4Å:- Chain A: P.612, W.613, N.614
Ligand excluded by PLIPNAG.52: 5 residues within 4Å:- Chain A: E.637, I.638, G.639, N.640, Y.641
Ligand excluded by PLIPNAG.53: 3 residues within 4Å:- Chain D: K.180, N.182, S.183
Ligand excluded by PLIPNAG.54: 5 residues within 4Å:- Chain D: N.296, I.317, G.433, N.434
- Ligands: NAG.56
Ligand excluded by PLIPNAG.55: 4 residues within 4Å:- Chain D: R.349, N.389, N.391, D.392
Ligand excluded by PLIPNAG.56: 2 residues within 4Å:- Chain D: N.434
- Ligands: NAG.54
Ligand excluded by PLIPNAG.57: 4 residues within 4Å:- Chain D: N.257, S.286, N.440
- Ligands: NAG-NAG-BMA-MAN-MAN.23
Ligand excluded by PLIPNAG.58: 3 residues within 4Å:- Chain D: P.612, W.613, N.614
Ligand excluded by PLIPNAG.59: 5 residues within 4Å:- Chain D: E.637, I.638, G.639, N.640, Y.641
Ligand excluded by PLIPNAG.60: 3 residues within 4Å:- Chain G: K.180, N.182, S.183
Ligand excluded by PLIPNAG.61: 5 residues within 4Å:- Chain G: N.296, I.317, G.433, N.434
- Ligands: NAG.63
Ligand excluded by PLIPNAG.62: 4 residues within 4Å:- Chain G: R.349, N.389, N.391, D.392
Ligand excluded by PLIPNAG.63: 2 residues within 4Å:- Chain G: N.434
- Ligands: NAG.61
Ligand excluded by PLIPNAG.64: 4 residues within 4Å:- Chain G: N.257, S.286, N.440
- Ligands: NAG-NAG-BMA-MAN-MAN.38
Ligand excluded by PLIPNAG.65: 3 residues within 4Å:- Chain G: P.612, W.613, N.614
Ligand excluded by PLIPNAG.66: 5 residues within 4Å:- Chain G: E.637, I.638, G.639, N.640, Y.641
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dubrovskaya, V. et al., Vaccination with Glycan-Modified HIV NFL Envelope Trimer-Liposomes Elicits Broadly Neutralizing Antibodies to Multiple Sites of Vulnerability. Immunity (2019)
- Release Date
- 2019-11-20
- Peptides
- HIV Env 16055 NFL TD 2CC+: ADG
Rabbit antibody 1C2 heavy chain fragment antigen binding: BEH
Rabbit antibody 1C2 kappa chain: CFI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
BG
EB
HE
CH
FC
LF
DI
G
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.94 Å
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 6 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
- 33 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 3 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
- 3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
- 21 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dubrovskaya, V. et al., Vaccination with Glycan-Modified HIV NFL Envelope Trimer-Liposomes Elicits Broadly Neutralizing Antibodies to Multiple Sites of Vulnerability. Immunity (2019)
- Release Date
- 2019-11-20
- Peptides
- HIV Env 16055 NFL TD 2CC+: ADG
Rabbit antibody 1C2 heavy chain fragment antigen binding: BEH
Rabbit antibody 1C2 kappa chain: CFI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
BG
EB
HE
CH
FC
LF
DI
G