- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.30 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
- 8 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.65, W.357
- Chain C: Y.386
No protein-ligand interaction detected (PLIP)NAG-NAG.3: 4 residues within 4Å:- Chain A: D.2, F.3, N.5, N.154
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.2
- Water bridges: A:N.154, A:N.154
NAG-NAG.12: 3 residues within 4Å:- Chain B: N.65, W.357
- Chain D: Y.386
No protein-ligand interaction detected (PLIP)NAG-NAG.13: 4 residues within 4Å:- Chain B: D.2, F.3, N.5, N.154
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:D.2
- Water bridges: B:N.154, B:N.154
NAG-NAG.22: 3 residues within 4Å:- Chain B: Y.386
- Chain C: N.65, W.357
No protein-ligand interaction detected (PLIP)NAG-NAG.23: 4 residues within 4Å:- Chain C: D.2, F.3, N.5, N.154
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:D.2
- Water bridges: C:N.154, C:N.154
NAG-NAG.32: 3 residues within 4Å:- Chain A: Y.386
- Chain D: N.65, W.357
No protein-ligand interaction detected (PLIP)NAG-NAG.33: 4 residues within 4Å:- Chain D: D.2, F.3, N.5, N.154
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:D.2
- Water bridges: D:N.154, D:N.154
- 8 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)
CA.4: 3 residues within 4Å:- Ligands: CA.14, CA.24, CA.34
No protein-ligand interaction detected (PLIP)CA.5: 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.1, H2O.11
CA.14: 3 residues within 4Å:- Ligands: CA.4, CA.24, CA.34
No protein-ligand interaction detected (PLIP)CA.15: 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.28, H2O.38
CA.24: 3 residues within 4Å:- Ligands: CA.4, CA.14, CA.34
No protein-ligand interaction detected (PLIP)CA.25: 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.54, H2O.64
CA.34: 3 residues within 4Å:- Ligands: CA.4, CA.14, CA.24
No protein-ligand interaction detected (PLIP)CA.35: 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.81, H2O.91
- 12 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 6 residues within 4Å:- Chain A: C.11, A.333, E.334, G.335, C.337, R.339
4 PLIP interactions:1 interactions with chain D, 3 interactions with chain A- Water bridges: D:V.132, A:E.336, A:R.339
- Hydrogen bonds: A:R.339
GOL.7: 7 residues within 4Å:- Chain A: R.26
- Chain D: H.63, N.65, G.66, H.69, S.72, Y.74
8 PLIP interactions:6 interactions with chain D, 2 interactions with chain A- Hydrogen bonds: D:H.63, A:R.26, A:R.26
- Water bridges: D:Q.55, D:Q.55, D:H.63, D:S.72, D:Y.74
GOL.8: 3 residues within 4Å:- Chain A: H.69, D.70, R.71
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:D.70, A:D.70, A:R.71, A:R.71
- Water bridges: A:D.70
GOL.16: 6 residues within 4Å:- Chain B: C.11, A.333, E.334, G.335, C.337, R.339
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:R.339
- Water bridges: B:E.336, B:R.339, C:V.132
GOL.17: 7 residues within 4Å:- Chain B: R.26
- Chain C: H.63, N.65, G.66, H.69, S.72, Y.74
8 PLIP interactions:6 interactions with chain C, 2 interactions with chain B- Hydrogen bonds: C:H.63, B:R.26, B:R.26
- Water bridges: C:Q.55, C:Q.55, C:H.63, C:S.72, C:Y.74
GOL.18: 3 residues within 4Å:- Chain B: H.69, D.70, R.71
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:D.70, B:D.70, B:R.71, B:R.71
- Water bridges: B:D.70
GOL.26: 6 residues within 4Å:- Chain C: C.11, A.333, E.334, G.335, C.337, R.339
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:R.339
- Water bridges: C:E.336, C:R.339, A:V.132
GOL.27: 7 residues within 4Å:- Chain A: H.63, N.65, G.66, H.69, S.72, Y.74
- Chain C: R.26
8 PLIP interactions:6 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: A:H.63, C:R.26, C:R.26
- Water bridges: A:Q.55, A:Q.55, A:H.63, A:S.72, A:Y.74
GOL.28: 3 residues within 4Å:- Chain C: H.69, D.70, R.71
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:D.70, C:D.70, C:R.71, C:R.71
- Water bridges: C:D.70
GOL.36: 6 residues within 4Å:- Chain D: C.11, A.333, E.334, G.335, C.337, R.339
4 PLIP interactions:1 interactions with chain B, 3 interactions with chain D- Water bridges: B:V.132, D:E.336, D:R.339
- Hydrogen bonds: D:R.339
GOL.37: 7 residues within 4Å:- Chain B: H.63, N.65, G.66, H.69, S.72, Y.74
- Chain D: R.26
8 PLIP interactions:2 interactions with chain D, 6 interactions with chain B- Hydrogen bonds: D:R.26, D:R.26, B:H.63
- Water bridges: B:Q.55, B:Q.55, B:H.63, B:S.72, B:Y.74
GOL.38: 3 residues within 4Å:- Chain D: H.69, D.70, R.71
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:D.70, D:D.70, D:R.71, D:R.71
- Water bridges: D:D.70
- 4 x ZMR: ZANAMIVIR(Non-covalent)
ZMR.9: 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
22 PLIP interactions:22 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:R.144, A:E.197, A:R.212, A:R.212
- Water bridges: A:R.75, A:R.75, A:R.144, A:E.147, A:E.197, A:R.290
- Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.212, A:R.290
ZMR.19: 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
22 PLIP interactions:22 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:R.144, B:E.197, B:R.212, B:R.212
- Water bridges: B:R.75, B:R.75, B:R.144, B:E.147, B:E.197, B:R.290
- Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.212, B:R.290
ZMR.29: 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
22 PLIP interactions:22 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:R.144, C:E.197, C:R.212, C:R.212
- Water bridges: C:R.75, C:R.75, C:R.144, C:E.147, C:E.197, C:R.290
- Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.212, C:R.290
ZMR.39: 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
22 PLIP interactions:22 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:R.144, D:E.197, D:R.212, D:R.212
- Water bridges: D:R.75, D:R.75, D:R.144, D:E.147, D:E.197, D:R.290
- Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.212, D:R.290
- 4 x K: POTASSIUM ION(Non-functional Binders)
K.10: 3 residues within 4Å:- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1
No protein-ligand interaction detected (PLIP)K.20: 3 residues within 4Å:- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11
No protein-ligand interaction detected (PLIP)K.30: 3 residues within 4Å:- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.21, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.21, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.21
No protein-ligand interaction detected (PLIP)K.40: 3 residues within 4Å:- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.31
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Salinger, M.T. et al., High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. (In preparation). To Be Published
- Release Date
- 2018-08-29
- Peptides
- Neuraminidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.30 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
- 8 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 8 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)
- 12 x GOL: GLYCEROL(Non-functional Binders)
- 4 x ZMR: ZANAMIVIR(Non-covalent)
- 4 x K: POTASSIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Salinger, M.T. et al., High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. (In preparation). To Be Published
- Release Date
- 2018-08-29
- Peptides
- Neuraminidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A