- 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- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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
- 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.15: 3 residues within 4Å:- Chain B: N.65, W.357
- Chain D: Y.386
No protein-ligand interaction detected (PLIP)NAG-NAG.16: 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.28: 3 residues within 4Å:- Chain B: Y.386
- Chain C: N.65, W.357
No protein-ligand interaction detected (PLIP)NAG-NAG.29: 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.41: 3 residues within 4Å:- Chain A: Y.386
- Chain D: N.65, W.357
No protein-ligand interaction detected (PLIP)NAG-NAG.42: 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.17, CA.30, CA.43
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.2, H2O.9
CA.17: 3 residues within 4Å:- Ligands: CA.4, CA.30, CA.43
No protein-ligand interaction detected (PLIP)CA.18: 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.30, H2O.37
CA.30: 3 residues within 4Å:- Ligands: CA.4, CA.17, CA.43
No protein-ligand interaction detected (PLIP)CA.31: 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.58, H2O.65
CA.43: 3 residues within 4Å:- Ligands: CA.4, CA.17, CA.30
No protein-ligand interaction detected (PLIP)CA.44: 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.86, H2O.93
- 16 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 5 residues within 4Å:- Chain A: A.333, E.334, G.335, C.337, R.339
Ligand excluded by PLIPGOL.7: 6 residues within 4Å:- Chain A: R.26
- Chain D: H.63, N.65, G.66, T.67, Y.74
Ligand excluded by PLIPGOL.8: 4 residues within 4Å:- Chain A: H.69, D.70, R.71
- Ligands: PO4.10
Ligand excluded by PLIPGOL.9: 5 residues within 4Å:- Chain A: L.188, A.189, G.190, A.192, K.193
Ligand excluded by PLIPGOL.19: 5 residues within 4Å:- Chain B: A.333, E.334, G.335, C.337, R.339
Ligand excluded by PLIPGOL.20: 6 residues within 4Å:- Chain B: R.26
- Chain C: H.63, N.65, G.66, T.67, Y.74
Ligand excluded by PLIPGOL.21: 4 residues within 4Å:- Chain B: H.69, D.70, R.71
- Ligands: PO4.23
Ligand excluded by PLIPGOL.22: 5 residues within 4Å:- Chain B: L.188, A.189, G.190, A.192, K.193
Ligand excluded by PLIPGOL.32: 5 residues within 4Å:- Chain C: A.333, E.334, G.335, C.337, R.339
Ligand excluded by PLIPGOL.33: 6 residues within 4Å:- Chain A: H.63, N.65, G.66, T.67, Y.74
- Chain C: R.26
Ligand excluded by PLIPGOL.34: 4 residues within 4Å:- Chain C: H.69, D.70, R.71
- Ligands: PO4.36
Ligand excluded by PLIPGOL.35: 5 residues within 4Å:- Chain C: L.188, A.189, G.190, A.192, K.193
Ligand excluded by PLIPGOL.45: 5 residues within 4Å:- Chain D: A.333, E.334, G.335, C.337, R.339
Ligand excluded by PLIPGOL.46: 6 residues within 4Å:- Chain B: H.63, N.65, G.66, T.67, Y.74
- Chain D: R.26
Ligand excluded by PLIPGOL.47: 4 residues within 4Å:- Chain D: H.69, D.70, R.71
- Ligands: PO4.49
Ligand excluded by PLIPGOL.48: 5 residues within 4Å:- Chain D: L.188, A.189, G.190, A.192, K.193
Ligand excluded by PLIP- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.10: 3 residues within 4Å:- Chain A: H.69, R.71
- Ligands: GOL.8
8 PLIP interactions:8 interactions with chain A- Water bridges: A:H.69, A:D.70, A:R.71, A:R.71, A:N.118, A:N.118
- Salt bridges: A:H.69, A:R.71
PO4.23: 3 residues within 4Å:- Chain B: H.69, R.71
- Ligands: GOL.21
8 PLIP interactions:8 interactions with chain B- Water bridges: B:H.69, B:D.70, B:R.71, B:R.71, B:N.118, B:N.118
- Salt bridges: B:H.69, B:R.71
PO4.36: 3 residues within 4Å:- Chain C: H.69, R.71
- Ligands: GOL.34
8 PLIP interactions:8 interactions with chain C- Water bridges: C:H.69, C:D.70, C:R.71, C:R.71, C:N.118, C:N.118
- Salt bridges: C:H.69, C:R.71
PO4.49: 3 residues within 4Å:- Chain D: H.69, R.71
- Ligands: GOL.47
8 PLIP interactions:8 interactions with chain D- Water bridges: D:H.69, D:D.70, D:R.71, D:R.71, D:N.118, D:N.118
- Salt bridges: D:H.69, D:R.71
- 8 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)
SIA.11: 14 residues within 4Å:- Chain A: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.290, Y.324
17 PLIP interactions:17 interactions with chain A- Hydrophobic interactions: A:W.98, A:I.142, A:R.144
- Hydrogen bonds: A:E.38, A:D.70, A:R.71, A:R.144, A:E.197, A:R.212, A:R.212
- Water bridges: A:R.75, A:E.197, A:E.197, A:E.197
- Salt bridges: A:R.37, A:R.212, A:R.290
SIA.12: 9 residues within 4Å:- Chain A: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352
13 PLIP interactions:13 interactions with chain A- Hydrophobic interactions: A:W.321
- Hydrogen bonds: A:S.286, A:S.286, A:S.291, A:S.291, A:N.318, A:N.318, A:K.352
- Water bridges: A:I.287, A:A.288, A:N.318, A:K.352, A:K.352
SIA.24: 14 residues within 4Å:- Chain B: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.290, Y.324
17 PLIP interactions:17 interactions with chain B- Hydrophobic interactions: B:W.98, B:I.142, B:R.144
- Hydrogen bonds: B:E.38, B:D.70, B:R.71, B:R.144, B:E.197, B:R.212, B:R.212
- Water bridges: B:R.75, B:E.197, B:E.197, B:E.197
- Salt bridges: B:R.37, B:R.212, B:R.290
SIA.25: 9 residues within 4Å:- Chain B: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352
13 PLIP interactions:13 interactions with chain B- Hydrophobic interactions: B:W.321
- Hydrogen bonds: B:S.286, B:S.286, B:S.291, B:S.291, B:N.318, B:N.318, B:K.352
- Water bridges: B:I.287, B:A.288, B:N.318, B:K.352, B:K.352
SIA.37: 14 residues within 4Å:- Chain C: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.290, Y.324
17 PLIP interactions:17 interactions with chain C- Hydrophobic interactions: C:W.98, C:I.142, C:R.144
- Hydrogen bonds: C:E.38, C:D.70, C:R.71, C:R.144, C:E.197, C:R.212, C:R.212
- Water bridges: C:R.75, C:E.197, C:E.197, C:E.197
- Salt bridges: C:R.37, C:R.212, C:R.290
SIA.38: 9 residues within 4Å:- Chain C: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352
13 PLIP interactions:13 interactions with chain C- Hydrophobic interactions: C:W.321
- Hydrogen bonds: C:S.286, C:S.286, C:S.291, C:S.291, C:N.318, C:N.318, C:K.352
- Water bridges: C:I.287, C:A.288, C:N.318, C:K.352, C:K.352
SIA.50: 14 residues within 4Å:- Chain D: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.290, Y.324
17 PLIP interactions:17 interactions with chain D- Hydrophobic interactions: D:W.98, D:I.142, D:R.144
- Hydrogen bonds: D:E.38, D:D.70, D:R.71, D:R.144, D:E.197, D:R.212, D:R.212
- Water bridges: D:R.75, D:E.197, D:E.197, D:E.197
- Salt bridges: D:R.37, D:R.212, D:R.290
SIA.51: 9 residues within 4Å:- Chain D: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352
13 PLIP interactions:13 interactions with chain D- Hydrophobic interactions: D:W.321
- Hydrogen bonds: D:S.286, D:S.286, D:S.291, D:S.291, D:N.318, D:N.318, D:K.352
- Water bridges: D:I.287, D:A.288, D:N.318, D:K.352, D:K.352
- 4 x K: POTASSIUM ION(Non-functional Binders)
K.13: 3 residues within 4Å:- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1
No protein-ligand interaction detected (PLIP)K.26: 3 residues within 4Å:- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.14
No protein-ligand interaction detected (PLIP)K.39: 3 residues within 4Å:- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.27, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.27, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.27
No protein-ligand interaction detected (PLIP)K.52: 3 residues within 4Å:- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.40, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.40, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.40
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- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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
- 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)
- 16 x GOL: GLYCEROL(Non-functional Binders)
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 8 x SIA: N-acetyl-alpha-neuraminic acid(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