- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 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
- 4 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: 4 residues within 4Å:- Chain A: D.2, F.3, N.5, N.154
No protein-ligand interaction detected (PLIP)NAG-NAG.14: 4 residues within 4Å:- Chain B: D.2, F.3, N.5, N.154
No protein-ligand interaction detected (PLIP)NAG-NAG.26: 4 residues within 4Å:- Chain C: D.2, F.3, N.5, N.154
No protein-ligand interaction detected (PLIP)NAG-NAG.38: 4 residues within 4Å:- Chain D: D.2, F.3, N.5, N.154
No protein-ligand interaction detected (PLIP)- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.3: 2 residues within 4Å:- Chain A: N.65, W.357
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.65, A:W.357
NAG.15: 2 residues within 4Å:- Chain B: N.65, W.357
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.65, B:W.357
NAG.27: 2 residues within 4Å:- Chain C: N.65, W.357
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.65, C:W.357
NAG.39: 2 residues within 4Å:- Chain D: N.65, W.357
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:N.65, D:W.357
- 28 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 7 residues within 4Å:- Chain A: H.63, N.65, G.66, T.67, S.72, Y.74
- Chain C: R.26
Ligand excluded by PLIPGOL.5: 6 residues within 4Å:- Chain A: C.11, A.333, E.334, G.335, C.337, R.339
Ligand excluded by PLIPGOL.6: 12 residues within 4Å:- Chain A: L.34, S.54, G.56, Y.74, R.75, A.76, I.96
- Chain C: K.21, D.22, N.23, I.27, S.83
Ligand excluded by PLIPGOL.7: 5 residues within 4Å:- Chain A: L.188, A.189, G.190, A.192, K.193
Ligand excluded by PLIPGOL.8: 4 residues within 4Å:- Chain A: S.286, A.288, S.289, N.318
Ligand excluded by PLIPGOL.9: 4 residues within 4Å:- Chain A: K.255, C.256, N.257, D.258
Ligand excluded by PLIPGOL.10: 3 residues within 4Å:- Chain A: H.69, D.70, R.71
Ligand excluded by PLIPGOL.16: 7 residues within 4Å:- Chain B: H.63, N.65, G.66, T.67, S.72, Y.74
- Chain D: R.26
Ligand excluded by PLIPGOL.17: 6 residues within 4Å:- Chain B: C.11, A.333, E.334, G.335, C.337, R.339
Ligand excluded by PLIPGOL.18: 12 residues within 4Å:- Chain B: L.34, S.54, G.56, Y.74, R.75, A.76, I.96
- Chain D: K.21, D.22, N.23, I.27, S.83
Ligand excluded by PLIPGOL.19: 5 residues within 4Å:- Chain B: L.188, A.189, G.190, A.192, K.193
Ligand excluded by PLIPGOL.20: 4 residues within 4Å:- Chain B: S.286, A.288, S.289, N.318
Ligand excluded by PLIPGOL.21: 4 residues within 4Å:- Chain B: K.255, C.256, N.257, D.258
Ligand excluded by PLIPGOL.22: 3 residues within 4Å:- Chain B: H.69, D.70, R.71
Ligand excluded by PLIPGOL.28: 7 residues within 4Å:- Chain B: R.26
- Chain C: H.63, N.65, G.66, T.67, S.72, Y.74
Ligand excluded by PLIPGOL.29: 6 residues within 4Å:- Chain C: C.11, A.333, E.334, G.335, C.337, R.339
Ligand excluded by PLIPGOL.30: 12 residues within 4Å:- Chain B: K.21, D.22, N.23, I.27, S.83
- Chain C: L.34, S.54, G.56, Y.74, R.75, A.76, I.96
Ligand excluded by PLIPGOL.31: 5 residues within 4Å:- Chain C: L.188, A.189, G.190, A.192, K.193
Ligand excluded by PLIPGOL.32: 4 residues within 4Å:- Chain C: S.286, A.288, S.289, N.318
Ligand excluded by PLIPGOL.33: 4 residues within 4Å:- Chain C: K.255, C.256, N.257, D.258
Ligand excluded by PLIPGOL.34: 3 residues within 4Å:- Chain C: H.69, D.70, R.71
Ligand excluded by PLIPGOL.40: 7 residues within 4Å:- Chain A: R.26
- Chain D: H.63, N.65, G.66, T.67, S.72, Y.74
Ligand excluded by PLIPGOL.41: 6 residues within 4Å:- Chain D: C.11, A.333, E.334, G.335, C.337, R.339
Ligand excluded by PLIPGOL.42: 12 residues within 4Å:- Chain A: K.21, D.22, N.23, I.27, S.83
- Chain D: L.34, S.54, G.56, Y.74, R.75, A.76, I.96
Ligand excluded by PLIPGOL.43: 5 residues within 4Å:- Chain D: L.188, A.189, G.190, A.192, K.193
Ligand excluded by PLIPGOL.44: 4 residues within 4Å:- Chain D: S.286, A.288, S.289, N.318
Ligand excluded by PLIPGOL.45: 4 residues within 4Å:- Chain D: K.255, C.256, N.257, D.258
Ligand excluded by PLIPGOL.46: 3 residues within 4Å:- Chain D: H.69, D.70, R.71
Ligand excluded by PLIP- 4 x ZGE: 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-3-fluoro-D-glycero-D-galacto-non-2-enonic acid(Post Translational Modification)
ZGE.11: 15 residues within 4Å:- Chain A: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, R.290, Y.324
23 PLIP interactions:23 interactions with chain A- Hydrophobic interactions: A:W.98, A:I.142, A:R.144
- Hydrogen bonds: A:R.71, A:W.98, A:W.98, A:E.197, A:R.212
- Water bridges: A:R.37, A:R.75, A:R.144, A:E.147, A:E.197, A:E.197, A:R.212, A:R.212
- Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.212, A:R.290
- Halogen bonds: A:R.37
ZGE.23: 15 residues within 4Å:- Chain B: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, R.290, Y.324
23 PLIP interactions:23 interactions with chain B- Hydrophobic interactions: B:W.98, B:I.142, B:R.144
- Hydrogen bonds: B:R.71, B:W.98, B:W.98, B:E.197, B:R.212
- Water bridges: B:R.37, B:R.75, B:R.144, B:E.147, B:E.197, B:E.197, B:R.212, B:R.212
- Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.212, B:R.290
- Halogen bonds: B:R.37
ZGE.35: 15 residues within 4Å:- Chain C: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, R.290, Y.324
23 PLIP interactions:23 interactions with chain C- Hydrophobic interactions: C:W.98, C:I.142, C:R.144
- Hydrogen bonds: C:R.71, C:W.98, C:W.98, C:E.197, C:R.212
- Water bridges: C:R.37, C:R.75, C:R.144, C:E.147, C:E.197, C:E.197, C:R.212, C:R.212
- Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.212, C:R.290
- Halogen bonds: C:R.37
ZGE.47: 15 residues within 4Å:- Chain D: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, R.290, Y.324
23 PLIP interactions:23 interactions with chain D- Hydrophobic interactions: D:W.98, D:I.142, D:R.144
- Hydrogen bonds: D:R.71, D:W.98, D:W.98, D:E.197, D:R.212
- Water bridges: D:R.37, D:R.75, D:R.144, D:E.147, D:E.197, D:E.197, D:R.212, D:R.212
- Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.212, D:R.290
- Halogen bonds: D:R.37
- 4 x CA: CALCIUM ION(Non-covalent)
CA.12: 5 residues within 4Å:- Chain A: D.213, G.217, D.244, N.266, G.267
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.213, A:G.217, A:D.244, H2O.7, H2O.9
CA.24: 5 residues within 4Å:- Chain B: D.213, G.217, D.244, N.266, G.267
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.213, B:G.217, B:D.244, H2O.21, H2O.24
CA.36: 5 residues within 4Å:- Chain C: D.213, G.217, D.244, N.266, G.267
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.213, C:G.217, C:D.244, H2O.36, H2O.39
CA.48: 5 residues within 4Å:- Chain D: D.213, G.217, D.244, N.266, G.267
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.213, D:G.217, D:D.244, H2O.51, H2O.54
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kim, J.-H. et al., Mechanism-based covalent neuraminidase inhibitors with broad-spectrum influenza antiviral activity. Science (2013)
- Release Date
- 2013-05-01
- Peptides
- Neuraminidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 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
- 4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 28 x GOL: GLYCEROL(Non-functional Binders)
- 4 x ZGE: 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-3-fluoro-D-glycero-D-galacto-non-2-enonic acid(Post Translational Modification)
- 4 x CA: CALCIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kim, J.-H. et al., Mechanism-based covalent neuraminidase inhibitors with broad-spectrum influenza antiviral activity. Science (2013)
- Release Date
- 2013-05-01
- Peptides
- Neuraminidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A