- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.39 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
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.2
NAG-NAG.9: 4 residues within 4Å:- Chain B: D.2, F.3, N.5, N.154
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:D.2
NAG-NAG.16: 4 residues within 4Å:- Chain C: D.2, F.3, N.5, N.154
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:D.2
NAG-NAG.23: 4 residues within 4Å:- Chain D: D.2, F.3, N.5, N.154
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:D.2
- 4 x 9T7: (2R,3R,4R,5R,6R)-5-acetamido-6-[(1R,2R)-1,2-bis(oxidanyl)propyl]-2,3-bis(fluoranyl)-4-oxidanyl-oxane-2-carboxylic acid(Non-covalent)
9T7.3: 9 residues within 4Å:- Chain A: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:W.321
- Hydrogen bonds: A:S.286, A:S.289, A:S.289, A:S.291, A:S.291, A:N.318
- Water bridges: A:I.287
9T7.10: 9 residues within 4Å:- Chain B: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:W.321
- Hydrogen bonds: B:S.286, B:S.289, B:S.289, B:S.291, B:S.291, B:N.318
- Water bridges: B:I.287
9T7.17: 9 residues within 4Å:- Chain C: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352
8 PLIP interactions:8 interactions with chain C- Hydrophobic interactions: C:W.321
- Hydrogen bonds: C:S.286, C:S.289, C:S.289, C:S.291, C:S.291, C:N.318
- Water bridges: C:I.287
9T7.24: 9 residues within 4Å:- Chain D: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:W.321
- Hydrogen bonds: D:S.286, D:S.289, D:S.289, D:S.291, D:S.291, D:N.318
- Water bridges: D:I.287
- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.4: 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.11: 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.18: 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.25: 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
- 4 x CA: CALCIUM ION(Non-covalent)
CA.5: 4 residues within 4Å:- Chain A: D.213, G.217, D.244, N.266
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.8
CA.12: 4 residues within 4Å:- Chain B: D.213, G.217, D.244, N.266
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.213, B:G.217, B:D.244, H2O.15, H2O.22
CA.19: 4 residues within 4Å:- Chain C: D.213, G.217, D.244, N.266
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.213, C:G.217, C:D.244, H2O.29, H2O.35
CA.26: 4 residues within 4Å:- Chain D: D.213, G.217, D.244, N.266
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.213, D:G.217, D:D.244, H2O.42, H2O.49
- 4 x 9TM: (2~{R},3~{R},4~{R},5~{R})-3-acetamido-2-[(1~{R},2~{R})-1,2-bis(oxidanyl)propyl]-5-fluoranyl-4-oxidanyl-2,3,4,5-tetrahydropyran-1-ium-6-carboxylic acid(Non-covalent)
9TM.6: 12 residues within 4Å:- Chain A: R.37, E.38, D.70, R.71, R.144, A.166, E.196, E.197, R.212, R.290, Y.324
- Ligands: 9T1.7
14 PLIP interactions:14 interactions with chain A- Hydrophobic interactions: A:R.144, A:A.166
- Hydrogen bonds: A:E.38, A:R.71, A:E.197, A:E.197, A:E.197, A:R.212, A:R.212
- Water bridges: A:R.75
- Salt bridges: A:R.37, A:R.212, A:R.290
- Halogen bonds: A:D.70
9TM.13: 12 residues within 4Å:- Chain B: R.37, E.38, D.70, R.71, R.144, A.166, E.196, E.197, R.212, R.290, Y.324
- Ligands: 9T1.14
14 PLIP interactions:14 interactions with chain B- Hydrophobic interactions: B:R.144, B:A.166
- Hydrogen bonds: B:E.38, B:R.71, B:E.197, B:E.197, B:E.197, B:R.212, B:R.212
- Water bridges: B:R.75
- Salt bridges: B:R.37, B:R.212, B:R.290
- Halogen bonds: B:D.70
9TM.20: 12 residues within 4Å:- Chain C: R.37, E.38, D.70, R.71, R.144, A.166, E.196, E.197, R.212, R.290, Y.324
- Ligands: 9T1.21
14 PLIP interactions:14 interactions with chain C- Hydrophobic interactions: C:R.144, C:A.166
- Hydrogen bonds: C:E.38, C:R.71, C:E.197, C:E.197, C:E.197, C:R.212, C:R.212
- Water bridges: C:R.75
- Salt bridges: C:R.37, C:R.212, C:R.290
- Halogen bonds: C:D.70
9TM.27: 12 residues within 4Å:- Chain D: R.37, E.38, D.70, R.71, R.144, A.166, E.196, E.197, R.212, R.290, Y.324
- Ligands: 9T1.28
14 PLIP interactions:14 interactions with chain D- Hydrophobic interactions: D:R.144, D:A.166
- Hydrogen bonds: D:E.38, D:R.71, D:E.197, D:E.197, D:E.197, D:R.212, D:R.212
- Water bridges: D:R.75
- Salt bridges: D:R.37, D:R.212, D:R.290
- Halogen bonds: D:D.70
- 4 x 9T1: 5-acetamido-2,6-anhydro-3,5,9-trideoxy-3-fluoro-D-erythro-L-gluco-non-4-ulosonic acid(Post Translational Modification)
9T1.7: 12 residues within 4Å:- Chain A: R.37, E.38, D.70, R.71, W.98, I.142, E.196, E.197, R.212, R.290, Y.324
- Ligands: 9TM.6
15 PLIP interactions:15 interactions with chain A- Hydrophobic interactions: A:W.98, A:I.142
- Hydrogen bonds: A:R.71, A:E.197, A:R.212
- Water bridges: A:R.37, A:S.99, A:E.147, A:E.197, A:R.212, A:R.212
- Salt bridges: A:R.37, A:R.212, A:R.290
- Halogen bonds: A:R.37
9T1.14: 12 residues within 4Å:- Chain B: R.37, E.38, D.70, R.71, W.98, I.142, E.196, E.197, R.212, R.290, Y.324
- Ligands: 9TM.13
15 PLIP interactions:15 interactions with chain B- Hydrophobic interactions: B:W.98, B:I.142
- Hydrogen bonds: B:R.71, B:E.197, B:R.212
- Water bridges: B:R.37, B:S.99, B:E.147, B:E.197, B:R.212, B:R.212
- Salt bridges: B:R.37, B:R.212, B:R.290
- Halogen bonds: B:R.37
9T1.21: 12 residues within 4Å:- Chain C: R.37, E.38, D.70, R.71, W.98, I.142, E.196, E.197, R.212, R.290, Y.324
- Ligands: 9TM.20
15 PLIP interactions:15 interactions with chain C- Hydrophobic interactions: C:W.98, C:I.142
- Hydrogen bonds: C:R.71, C:E.197, C:R.212
- Water bridges: C:R.37, C:S.99, C:E.147, C:E.197, C:R.212, C:R.212
- Salt bridges: C:R.37, C:R.212, C:R.290
- Halogen bonds: C:R.37
9T1.28: 12 residues within 4Å:- Chain D: R.37, E.38, D.70, R.71, W.98, I.142, E.196, E.197, R.212, R.290, Y.324
- Ligands: 9TM.27
15 PLIP interactions:15 interactions with chain D- Hydrophobic interactions: D:W.98, D:I.142
- Hydrogen bonds: D:R.71, D:E.197, D:R.212
- Water bridges: D:R.37, D:S.99, D:E.147, D:E.197, D:R.212, D:R.212
- Salt bridges: D:R.37, D:R.212, D:R.290
- Halogen bonds: D:R.37
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- McKimm-Breschkin, J.L. et al., Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-acetylneuraminic Acid Derivatives. J. Med. Chem. (2018)
- Release Date
- 2018-02-21
- Peptides
- Neuraminidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.39 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 9T7: (2R,3R,4R,5R,6R)-5-acetamido-6-[(1R,2R)-1,2-bis(oxidanyl)propyl]-2,3-bis(fluoranyl)-4-oxidanyl-oxane-2-carboxylic acid(Non-covalent)
- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 x CA: CALCIUM ION(Non-covalent)
- 4 x 9TM: (2~{R},3~{R},4~{R},5~{R})-3-acetamido-2-[(1~{R},2~{R})-1,2-bis(oxidanyl)propyl]-5-fluoranyl-4-oxidanyl-2,3,4,5-tetrahydropyran-1-ium-6-carboxylic acid(Non-covalent)
- 4 x 9T1: 5-acetamido-2,6-anhydro-3,5,9-trideoxy-3-fluoro-D-erythro-L-gluco-non-4-ulosonic acid(Post Translational Modification)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- McKimm-Breschkin, J.L. et al., Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-acetylneuraminic Acid Derivatives. J. Med. Chem. (2018)
- Release Date
- 2018-02-21
- Peptides
- Neuraminidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A