- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-3-3-3-3-mer
- Ligands
- 3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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
- 15 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.114, E.117, R.120
No protein-ligand interaction detected (PLIP)NAG-NAG.8: 11 residues within 4Å:- Chain A: G.292, R.293, D.294, N.295, R.366, T.368, W.472, I.473, D.474
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.368
NAG-NAG.9: 2 residues within 4Å:- Chain A: N.316, D.456
No protein-ligand interaction detected (PLIP)NAG-NAG.11: 8 residues within 4Å:- Chain A: I.152, A.153, R.312, W.345, R.396, T.458, N.460
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:I.152, A:A.153
- Hydrogen bonds: A:R.312
NAG-NAG.12: 3 residues within 4Å:- Chain A: D.471, Q.477, N.479
No protein-ligand interaction detected (PLIP)NAG-NAG.27: 3 residues within 4Å:- Chain E: N.114, E.117, R.120
No protein-ligand interaction detected (PLIP)NAG-NAG.33: 11 residues within 4Å:- Chain E: G.292, R.293, D.294, N.295, R.366, T.368, W.472, I.473, D.474
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.26, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.26
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:T.368
NAG-NAG.34: 2 residues within 4Å:- Chain E: N.316, D.456
No protein-ligand interaction detected (PLIP)NAG-NAG.36: 8 residues within 4Å:- Chain E: I.152, A.153, R.312, W.345, R.396, T.458, N.460
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN.31
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:I.152, E:A.153
- Hydrogen bonds: E:R.312
NAG-NAG.37: 3 residues within 4Å:- Chain E: D.471, Q.477, N.479
No protein-ligand interaction detected (PLIP)NAG-NAG.52: 3 residues within 4Å:- Chain I: N.114, E.117, R.120
No protein-ligand interaction detected (PLIP)NAG-NAG.58: 11 residues within 4Å:- Chain I: G.292, R.293, D.294, N.295, R.366, T.368, W.472, I.473, D.474
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.51, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.51
1 PLIP interactions:1 interactions with chain I- Hydrogen bonds: I:T.368
NAG-NAG.59: 2 residues within 4Å:- Chain I: N.316, D.456
No protein-ligand interaction detected (PLIP)NAG-NAG.61: 8 residues within 4Å:- Chain I: I.152, A.153, R.312, W.345, R.396, T.458, N.460
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN.56
3 PLIP interactions:3 interactions with chain I- Hydrophobic interactions: I:I.152, I:A.153
- Hydrogen bonds: I:R.312
NAG-NAG.62: 3 residues within 4Å:- Chain I: D.471, Q.477, N.479
No protein-ligand interaction detected (PLIP)- 9 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.3: 3 residues within 4Å:- Chain A: M.144, N.146, T.148
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:M.144
NAG-NAG-FUC.4: 2 residues within 4Å:- Chain A: Q.154, N.156
No protein-ligand interaction detected (PLIP)NAG-NAG-FUC.5: 7 residues within 4Å:- Chain A: V.193, C.194, E.195, Q.196, N.212, T.213
- Chain E: K.176
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain E- Hydrogen bonds: A:Q.196, E:K.176
NAG-NAG-FUC.28: 3 residues within 4Å:- Chain E: M.144, N.146, T.148
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:M.144
NAG-NAG-FUC.29: 2 residues within 4Å:- Chain E: Q.154, N.156
No protein-ligand interaction detected (PLIP)NAG-NAG-FUC.30: 7 residues within 4Å:- Chain E: V.193, C.194, E.195, Q.196, N.212, T.213
- Chain I: K.176
2 PLIP interactions:1 interactions with chain I, 1 interactions with chain E- Hydrogen bonds: I:K.176, E:Q.196
NAG-NAG-FUC.53: 3 residues within 4Å:- Chain I: M.144, N.146, T.148
1 PLIP interactions:1 interactions with chain I- Hydrophobic interactions: I:M.144
NAG-NAG-FUC.54: 2 residues within 4Å:- Chain I: Q.154, N.156
No protein-ligand interaction detected (PLIP)NAG-NAG-FUC.55: 7 residues within 4Å:- Chain A: K.176
- Chain I: V.193, C.194, E.195, Q.196, N.212, T.213
2 PLIP interactions:1 interactions with chain I, 1 interactions with chain A- Hydrogen bonds: I:Q.196, A:K.176
- 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.6: 11 residues within 4Å:- Chain A: K.222, W.225, D.226, Q.270, N.278, N.394, R.396, C.459, N.460, S.461
- Ligands: NAG-NAG.11
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:N.460
- Hydrogen bonds: A:W.225, A:N.460
NAG-NAG-BMA-MAN-MAN-MAN.31: 11 residues within 4Å:- Chain E: K.222, W.225, D.226, Q.270, N.278, N.394, R.396, C.459, N.460, S.461
- Ligands: NAG-NAG.36
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:N.460
- Hydrogen bonds: E:W.225, E:N.460
NAG-NAG-BMA-MAN-MAN-MAN.56: 11 residues within 4Å:- Chain I: K.222, W.225, D.226, Q.270, N.278, N.394, R.396, C.459, N.460, S.461
- Ligands: NAG-NAG.61
3 PLIP interactions:3 interactions with chain I- Hydrophobic interactions: I:N.460
- Hydrogen bonds: I:W.225, I:N.460
- 3 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.7: 6 residues within 4Å:- Chain A: N.284, N.302, Y.304, Y.305, E.356
- Chain C: M.94
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:Y.304, A:Y.305
NAG-NAG-BMA-MAN-MAN.32: 6 residues within 4Å:- Chain E: N.284, N.302, Y.304, Y.305, E.356
- Chain G: M.94
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:Y.304, E:Y.305
NAG-NAG-BMA-MAN-MAN.57: 6 residues within 4Å:- Chain I: N.284, N.302, Y.304, Y.305, E.356
- Chain K: M.94
2 PLIP interactions:2 interactions with chain I- Hydrophobic interactions: I:Y.304, I:Y.305
- 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: 9 residues within 4Å:- Chain A: K.358, T.373, D.374, I.376, N.377, E.412, D.413, R.414, N.415
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.412, A:D.413
NAG-NAG-BMA.35: 9 residues within 4Å:- Chain E: K.358, T.373, D.374, I.376, N.377, E.412, D.413, R.414, N.415
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:E.412, E:D.413
NAG-NAG-BMA.60: 9 residues within 4Å:- Chain I: K.358, T.373, D.374, I.376, N.377, E.412, D.413, R.414, N.415
2 PLIP interactions:2 interactions with chain I- Hydrogen bonds: I:E.412, I:D.413
- 39 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.13: 3 residues within 4Å:- Chain A: N.70
- Chain B: G.15, S.16
Ligand excluded by PLIPNAG.14: 4 residues within 4Å:- Chain A: N.79, R.293
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1
Ligand excluded by PLIPNAG.15: 2 residues within 4Å:- Chain A: R.112, N.171
Ligand excluded by PLIPNAG.16: 3 residues within 4Å:- Chain A: E.182, Y.183, N.184
Ligand excluded by PLIPNAG.17: 2 residues within 4Å:- Chain A: G.197, N.198
Ligand excluded by PLIPNAG.18: 2 residues within 4Å:- Chain A: G.201, N.202
Ligand excluded by PLIPNAG.19: 4 residues within 4Å:- Chain A: E.66, A.68, N.244, V.259
Ligand excluded by PLIPNAG.20: 3 residues within 4Å:- Chain A: Y.304, N.306, K.349
Ligand excluded by PLIPNAG.21: 3 residues within 4Å:- Chain A: D.474, N.476, Q.477
Ligand excluded by PLIPNAG.22: 1 residues within 4Å:- Chain A: N.371
Ligand excluded by PLIPNAG.23: 6 residues within 4Å:- Chain B: P.99, N.100, S.102, F.121, L.122
- Ligands: NAG.25
Ligand excluded by PLIPNAG.24: 4 residues within 4Å:- Chain B: K.106, W.107, N.108, N.109
Ligand excluded by PLIPNAG.25: 4 residues within 4Å:- Chain B: F.121, L.122, N.125
- Ligands: NAG.23
Ligand excluded by PLIPNAG.38: 3 residues within 4Å:- Chain E: N.70
- Chain F: G.15, S.16
Ligand excluded by PLIPNAG.39: 4 residues within 4Å:- Chain E: N.79, R.293
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.26, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.26
Ligand excluded by PLIPNAG.40: 2 residues within 4Å:- Chain E: R.112, N.171
Ligand excluded by PLIPNAG.41: 3 residues within 4Å:- Chain E: E.182, Y.183, N.184
Ligand excluded by PLIPNAG.42: 2 residues within 4Å:- Chain E: G.197, N.198
Ligand excluded by PLIPNAG.43: 2 residues within 4Å:- Chain E: G.201, N.202
Ligand excluded by PLIPNAG.44: 4 residues within 4Å:- Chain E: E.66, A.68, N.244, V.259
Ligand excluded by PLIPNAG.45: 3 residues within 4Å:- Chain E: Y.304, N.306, K.349
Ligand excluded by PLIPNAG.46: 3 residues within 4Å:- Chain E: D.474, N.476, Q.477
Ligand excluded by PLIPNAG.47: 1 residues within 4Å:- Chain E: N.371
Ligand excluded by PLIPNAG.48: 6 residues within 4Å:- Chain F: P.99, N.100, S.102, F.121, L.122
- Ligands: NAG.50
Ligand excluded by PLIPNAG.49: 4 residues within 4Å:- Chain F: K.106, W.107, N.108, N.109
Ligand excluded by PLIPNAG.50: 4 residues within 4Å:- Chain F: F.121, L.122, N.125
- Ligands: NAG.48
Ligand excluded by PLIPNAG.63: 3 residues within 4Å:- Chain I: N.70
- Chain J: G.15, S.16
Ligand excluded by PLIPNAG.64: 4 residues within 4Å:- Chain I: N.79, R.293
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.51, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.51
Ligand excluded by PLIPNAG.65: 2 residues within 4Å:- Chain I: R.112, N.171
Ligand excluded by PLIPNAG.66: 3 residues within 4Å:- Chain I: E.182, Y.183, N.184
Ligand excluded by PLIPNAG.67: 2 residues within 4Å:- Chain I: G.197, N.198
Ligand excluded by PLIPNAG.68: 2 residues within 4Å:- Chain I: G.201, N.202
Ligand excluded by PLIPNAG.69: 4 residues within 4Å:- Chain I: E.66, A.68, N.244, V.259
Ligand excluded by PLIPNAG.70: 3 residues within 4Å:- Chain I: Y.304, N.306, K.349
Ligand excluded by PLIPNAG.71: 3 residues within 4Å:- Chain I: D.474, N.476, Q.477
Ligand excluded by PLIPNAG.72: 1 residues within 4Å:- Chain I: N.371
Ligand excluded by PLIPNAG.73: 6 residues within 4Å:- Chain J: P.99, N.100, S.102, F.121, L.122
- Ligands: NAG.75
Ligand excluded by PLIPNAG.74: 4 residues within 4Å:- Chain J: K.106, W.107, N.108, N.109
Ligand excluded by PLIPNAG.75: 4 residues within 4Å:- Chain J: F.121, L.122, N.125
- Ligands: NAG.73
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhao, F. et al., Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus. Nat Commun (2022)
- Release Date
- 2022-10-19
- Peptides
- Envelope glycoprotein gp120: AEI
Envelope glycoprotein gp41: BFJ
K11 Fab heavy chain: CGK
K11 Fab light chain: DHL - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
AI
AB
BF
BJ
BC
HG
HK
HD
LH
LL
L
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-3-3-3-3-mer
- Ligands
- 3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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
- 15 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 9 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
- 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
- 3 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
- 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
- 39 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhao, F. et al., Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus. Nat Commun (2022)
- Release Date
- 2022-10-19
- Peptides
- Envelope glycoprotein gp120: AEI
Envelope glycoprotein gp41: BFJ
K11 Fab heavy chain: CGK
K11 Fab light chain: DHL - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
AI
AB
BF
BJ
BC
HG
HK
HD
LH
LL
L