SMTL ID : 1nn2.1

THREE-DIMENSIONAL STRUCTURE OF THE NEURAMINIDASE OF INFLUENZA VIRUS A(SLASH)TOKYO(SLASH)3(SLASH)67 AT 2.2 ANGSTROMS RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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.1: 6 residues within 4Å: Chain A: E.2, N.5, S.7, Y.203 Ligands: NAG.4, NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain B: E.2, N.5, S.7, Y.203 Ligands: NAG.10, NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain C: E.2, N.5, S.7, Y.203 Ligands: NAG.16, NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain D: E.2, N.5, S.7, Y.203 Ligands: NAG.22, NAG.23 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN- NAG- NGK- FUL: 2-acetamido-2-deoxy-4-O-sulfo-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-NGK-FUL.2: 5 residues within 4Å: Chain A: N.65, W.356, I.388 Chain B: N.382, F.385 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.382 NAG-NAG-BMA-MAN-NAG-NGK-FUL.8: 5 residues within 4Å: Chain B: N.65, W.356, I.388 Chain D: N.382, F.385 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.382 NAG-NAG-BMA-MAN-NAG-NGK-FUL.14: 5 residues within 4Å: Chain A: N.382, F.385 Chain C: N.65, W.356, I.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.382 NAG-NAG-BMA-MAN-NAG-NGK-FUL.20: 5 residues within 4Å: Chain C: N.382, F.385 Chain D: N.65, W.356, I.388 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.382

4 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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

NAG-NAG-BMA-MAN-MAN-MAN.3: 9 residues within 4Å: Chain A: N.119 Chain B: T.14, Q.310, I.311, N.312, R.313, Y.372, G.373, T.374 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.312, B:N.312, B:R.313, B:Y.372, B:I.311, B:N.312, B:R.313 Water bridges: B:T.374 NAG-NAG-BMA-MAN-MAN-MAN.9: 9 residues within 4Å: Chain B: N.119 Chain D: T.14, Q.310, I.311, N.312, R.313, Y.372, G.373, T.374 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.312, D:N.312, D:R.313, D:Y.372, D:I.311, D:N.312, D:R.313 Water bridges: D:T.374 NAG-NAG-BMA-MAN-MAN-MAN.15: 9 residues within 4Å: Chain A: T.14, Q.310, I.311, N.312, R.313, Y.372, G.373, T.374 Chain C: N.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.312, A:N.312, A:R.313, A:Y.372, A:I.311, A:N.312, A:R.313 Water bridges: A:T.374 NAG-NAG-BMA-MAN-MAN-MAN.21: 9 residues within 4Å: Chain C: T.14, Q.310, I.311, N.312, R.313, Y.372, G.373, T.374 Chain D: N.119 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.312, C:N.312, C:R.313, C:Y.372, C:I.311, C:N.312, C:R.313 Water bridges: C:T.374

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.4: 9 residues within 4Å: Chain A: N.5, I.152, N.153, Y.203, P.204, M.226, E.227 Ligands: NAG-NAG.1, NAG.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.204, A:M.226, A:E.227 Hydrogen bonds: A:N.153, A:E.227 NAG.5: 2 residues within 4Å: Ligands: NAG-NAG.1, NAG.4 No protein-ligand interaction detected (PLIP) NAG.10: 9 residues within 4Å: Chain B: N.5, I.152, N.153, Y.203, P.204, M.226, E.227 Ligands: NAG-NAG.7, NAG.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.204, B:M.226, B:E.227 Hydrogen bonds: B:N.153, B:E.227 NAG.11: 2 residues within 4Å: Ligands: NAG-NAG.7, NAG.10 No protein-ligand interaction detected (PLIP) NAG.16: 9 residues within 4Å: Chain C: N.5, I.152, N.153, Y.203, P.204, M.226, E.227 Ligands: NAG-NAG.13, NAG.17 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:P.204, C:M.226, C:E.227 Hydrogen bonds: C:N.153, C:E.227 NAG.17: 2 residues within 4Å: Ligands: NAG-NAG.13, NAG.16 No protein-ligand interaction detected (PLIP) NAG.22: 9 residues within 4Å: Chain D: N.5, I.152, N.153, Y.203, P.204, M.226, E.227 Ligands: NAG-NAG.19, NAG.23 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:P.204, D:M.226, D:E.227 Hydrogen bonds: D:N.153, D:E.227 NAG.23: 2 residues within 4Å: Ligands: NAG-NAG.19, NAG.22 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.212, G.216, D.243, G.264, T.265, Q.266 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.212, A:G.216, A:G.264, A:Q.266 CA.12: 6 residues within 4Å: Chain B: D.212, G.216, D.243, G.264, T.265, Q.266 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.212, B:G.216, B:G.264, B:Q.266 CA.18: 6 residues within 4Å: Chain C: D.212, G.216, D.243, G.264, T.265, Q.266 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.212, C:G.216, C:G.264, C:Q.266 CA.24: 6 residues within 4Å: Chain D: D.212, G.216, D.243, G.264, T.265, Q.266 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.212, D:G.216, D:G.264, D:Q.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varghese, J.N. et al., Three-dimensional structure of the neuraminidase of influenza virus A/Tokyo/3/67 at 2.2 A resolution. J.Mol.Biol. (1991)

Release Date

1992-07-15

Peptides

NEURAMINIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

NEURAMINIDASE

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