- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- homo-tetramer
- Ligands
- 6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: 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
NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3: 19 residues within 4Å:- Chain A: N.119, N.120
- Chain C: N.14, S.15, D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, L.374, G.375, S.376
- Ligands: GOL.43, GOL.44
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:N.313, C:N.313, C:N.313, C:N.313, C:N.313, C:N.313, C:R.284
- Water bridges: C:K.288, C:K.288
- 1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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
NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 17 residues within 4Å:- Chain A: N.14, S.15, D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, R.373, L.374, G.375
- Chain B: N.119, N.120
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.313, A:N.313, A:N.313, A:R.373, A:R.373, A:N.313
- 2 x NAG- NAG- BMA- MAN- MAN- MAN: 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
NAG-NAG-BMA-MAN-MAN-MAN.8: 15 residues within 4Å:- Chain C: N.120
- Chain D: N.14, D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313, V.315, R.373, L.374, G.375, S.376
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:N.313, D:N.313, D:N.313, D:N.313, D:R.373, D:R.373, D:N.313, D:R.284
- Water bridges: D:D.250, D:R.284, D:K.288, D:K.288
NAG-NAG-BMA-MAN-MAN-MAN.9: 16 residues within 4Å:- Chain B: N.14, D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, L.374, G.375, S.376
- Chain D: N.120
- Ligands: PEG.34
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:N.313, B:N.313, B:N.313, B:D.250, B:R.284
- Water bridges: B:R.373, B:D.250, B:D.250, B:K.288, B:K.288, B:K.288
- 25 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 8 residues within 4Å:- Chain A: R.26
- Chain B: Q.55, H.63, N.65, G.66, T.67, S.72
- Ligands: PEG.33
Ligand excluded by PLIPGOL.12: 6 residues within 4Å:- Chain A: E.29, D.30, A.31, H.32, R.60
- Chain C: D.30
Ligand excluded by PLIPGOL.13: 6 residues within 4Å:- Chain A: R.144, A.166, E.196, E.197, R.212, N.214
Ligand excluded by PLIPGOL.14: 6 residues within 4Å:- Chain A: R.169, L.188, A.189, G.190, A.192, Q.193
Ligand excluded by PLIPGOL.15: 3 residues within 4Å:- Chain A: H.380
- Chain B: F.74
- Ligands: PEG.33
Ligand excluded by PLIPGOL.16: 4 residues within 4Å:- Chain A: G.204, G.205, V.206, D.226
Ligand excluded by PLIPGOL.22: 6 residues within 4Å:- Chain B: R.26
- Chain D: H.63, N.65, G.66, T.67, S.72
Ligand excluded by PLIPGOL.23: 8 residues within 4Å:- Chain B: D.70, R.71, W.98, S.99, I.142, R.144, E.147
- Ligands: GOL.24
Ligand excluded by PLIPGOL.24: 8 residues within 4Å:- Chain B: R.144, A.166, E.196, E.197, R.212, N.214, Y.325
- Ligands: GOL.23
Ligand excluded by PLIPGOL.25: 6 residues within 4Å:- Chain B: R.169, L.188, A.189, G.190, A.192, Q.193
Ligand excluded by PLIPGOL.26: 4 residues within 4Å:- Chain B: N.318, N.321, H.380
- Ligands: PEG.30
Ligand excluded by PLIPGOL.27: 4 residues within 4Å:- Chain B: D.44, Q.46, G.47, R.49
Ligand excluded by PLIPGOL.38: 5 residues within 4Å:- Chain A: H.63, N.65, G.66
- Chain C: R.26
- Ligands: PO4.18
Ligand excluded by PLIPGOL.39: 3 residues within 4Å:- Chain C: N.167, N.168, W.215
Ligand excluded by PLIPGOL.40: 7 residues within 4Å:- Chain C: R.169, A.170, L.188, A.189, G.190, A.192, Q.193
Ligand excluded by PLIPGOL.41: 7 residues within 4Å:- Chain C: D.70, R.71, R.75, W.98, S.99, R.144, E.147
Ligand excluded by PLIPGOL.42: 6 residues within 4Å:- Chain C: E.29, D.30, A.31, H.32, R.60
- Chain D: D.30
Ligand excluded by PLIPGOL.43: 7 residues within 4Å:- Chain C: R.284, I.286, E.295
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3, GOL.44
Ligand excluded by PLIPGOL.44: 7 residues within 4Å:- Chain C: R.247, R.284, I.286, K.288, E.295
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3, GOL.43
Ligand excluded by PLIPGOL.45: 5 residues within 4Å:- Chain C: D.44, G.47, C.48, R.49, E.81
Ligand excluded by PLIPGOL.52: 6 residues within 4Å:- Chain C: H.63, N.65, G.66, T.67, S.72
- Chain D: R.26
Ligand excluded by PLIPGOL.53: 7 residues within 4Å:- Chain D: R.144, A.166, E.196, E.197, R.212, N.214
- Ligands: GOL.54
Ligand excluded by PLIPGOL.54: 8 residues within 4Å:- Chain D: D.70, R.71, W.98, S.99, R.144, E.147, E.197
- Ligands: GOL.53
Ligand excluded by PLIPGOL.55: 7 residues within 4Å:- Chain D: R.169, A.170, L.188, A.189, G.190, A.192, Q.193
Ligand excluded by PLIPGOL.56: 5 residues within 4Å:- Chain D: D.44, Q.46, G.47, C.48, R.49
Ligand excluded by PLIP- 4 x CA: CALCIUM ION(Non-covalent)
CA.17: 5 residues within 4Å:- Chain A: D.213, G.217, D.244, P.267, G.268
6 PLIP interactions:4 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.213, A:G.217, A:D.244, A:P.267, H2O.3, H2O.8
CA.28: 4 residues within 4Å:- Chain B: D.213, G.217, D.244, P.267
6 PLIP interactions:4 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.213, B:G.217, B:D.244, B:P.267, H2O.22, H2O.24
CA.46: 4 residues within 4Å:- Chain C: D.213, G.217, D.244, P.267
6 PLIP interactions:4 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.213, C:G.217, C:D.244, C:P.267, H2O.37, H2O.38
CA.57: 5 residues within 4Å:- Chain D: D.213, G.217, D.244, P.267, G.268
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.213, D:G.217, D:D.244, H2O.50, H2O.54
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.18: 4 residues within 4Å:- Chain A: N.65, G.66
- Ligands: NAG-NAG.2, GOL.38
8 PLIP interactions:4 interactions with chain C, 4 interactions with chain A- Water bridges: C:Y.387, C:Y.387, C:Y.387, C:Y.387, A:N.65, A:N.65, A:N.65
- Hydrogen bonds: A:N.65
PO4.19: 4 residues within 4Å:- Chain A: E.186, A.189, T.231, H.232
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:H.232
- Salt bridges: A:H.232
PO4.29: 3 residues within 4Å:- Chain B: W.138, K.173, I.185
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:K.173
- 19 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.20: 8 residues within 4Å:- Chain A: E.81, Q.84, Y.89, N.90
- Chain B: Y.89, N.90, T.91, R.92
Ligand excluded by PLIPPEG.30: 6 residues within 4Å:- Chain B: N.321, H.380, G.382, A.383
- Chain D: F.74
- Ligands: GOL.26
Ligand excluded by PLIPPEG.31: 9 residues within 4Å:- Chain B: H.17, D.331, K.336, N.340, C.342, C.368, G.369
- Chain D: P.131, E.134
Ligand excluded by PLIPPEG.32: 5 residues within 4Å:- Chain B: E.384, I.386, Y.387
- Ligands: NAG-NAG.10, NAG-NAG.10
Ligand excluded by PLIPPEG.33: 6 residues within 4Å:- Chain A: W.377
- Chain B: R.71, S.72, P.73
- Ligands: GOL.11, GOL.15
Ligand excluded by PLIPPEG.34: 4 residues within 4Å:- Chain B: K.240, G.309, P.310
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN.9
Ligand excluded by PLIPPEG.35: 5 residues within 4Å:- Chain B: G.263, S.264, P.265, D.266, P.267
Ligand excluded by PLIPPEG.36: 3 residues within 4Å:- Chain B: K.181, I.182, Q.183
Ligand excluded by PLIPPEG.37: 6 residues within 4Å:- Chain B: A.139, N.141, G.164, P.165, R.169, A.170
Ligand excluded by PLIPPEG.47: 10 residues within 4Å:- Chain A: P.131, I.132, E.134
- Chain C: H.17, D.331, K.336, N.340, C.342, C.368, G.369
Ligand excluded by PLIPPEG.48: 5 residues within 4Å:- Chain D: E.384, I.386, Y.387
- Ligands: NAG-NAG.7, NAG-NAG.7
Ligand excluded by PLIPPEG.49: 2 residues within 4Å:- Chain C: P.9, E.337
Ligand excluded by PLIPPEG.50: 7 residues within 4Å:- Chain C: S.246, G.262, G.263, S.264, P.265, D.266, P.267
Ligand excluded by PLIPPEG.58: 6 residues within 4Å:- Chain D: I.135, P.136, S.137, W.138, K.173, I.185
Ligand excluded by PLIPPEG.59: 11 residues within 4Å:- Chain C: P.131
- Chain D: H.17, L.19, C.48, F.329, D.331, K.336, N.340, C.342, C.368, G.369
Ligand excluded by PLIPPEG.60: 5 residues within 4Å:- Chain D: R.1, Q.46, H.104, G.106, M.107
Ligand excluded by PLIPPEG.61: 5 residues within 4Å:- Chain D: Q.307, S.308, G.309, P.310, I.311
Ligand excluded by PLIPPEG.62: 6 residues within 4Å:- Chain D: A.139, N.141, G.164, P.165, R.169, A.170
Ligand excluded by PLIPPEG.63: 8 residues within 4Å:- Chain C: R.49, S.79, W.80, N.90, T.91, R.92
- Chain D: E.81, Q.84
Ligand excluded by PLIP- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.21: 3 residues within 4Å:- Chain B: T.2, N.5, K.154
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:T.2
- Hydrogen bonds: B:N.5
NAG.51: 4 residues within 4Å:- Chain D: T.2, F.3, N.5, K.154
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:T.2, D:F.3, D:N.5
- Water bridges: D:F.3, D:N.5
- 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
- 2018-09-05
- Peptides
- Neuraminidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- homo-tetramer
- Ligands
- 6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: 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
- 1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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
- 2 x NAG- NAG- BMA- MAN- MAN- MAN: 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
- 25 x GOL: GLYCEROL(Non-functional Binders)
- 4 x CA: CALCIUM ION(Non-covalent)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
- 19 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 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
- 2018-09-05
- Peptides
- Neuraminidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D