SMTL ID : 1f8c.1

Native Influenza Neuraminidase in Complex with 4-amino-2-deoxy-2,3-dehydro-N-neuraminic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG-NAG-MAN-MAN-MAN-MAN-MAN.1: 20 residues within 4Å: Chain A: N.119, N.120, R.140 Chain C: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.372 Hydrogen bonds: C:G.312, C:Q.375 Water bridges: C:Q.311, C:G.312 NAG-NAG-MAN-MAN-MAN-MAN-MAN.7: 20 residues within 4Å: Chain B: N.119, N.120, R.140 Chain D: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.372 Hydrogen bonds: D:G.312, D:Q.375 Water bridges: D:Q.311, D:G.312 NAG-NAG-MAN-MAN-MAN-MAN-MAN.13: 20 residues within 4Å: Chain B: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain C: N.119, N.120, R.140 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.372 Hydrogen bonds: B:G.312, B:Q.375 Water bridges: B:Q.311, B:G.312 NAG-NAG-MAN-MAN-MAN-MAN-MAN.19: 20 residues within 4Å: Chain A: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain D: N.119, N.120, R.140 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.372 Hydrogen bonds: A:G.312, A:Q.375 Water bridges: A:Q.311, A:G.312

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.2 Water bridges: A:N.154 NAG-NAG.8: 4 residues within 4Å: Chain B: D.2, F.3, N.5, N.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.2 Water bridges: B:N.154 NAG-NAG.14: 4 residues within 4Å: Chain C: D.2, F.3, N.5, N.154 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.2 Water bridges: C:N.154 NAG-NAG.20: 4 residues within 4Å: Chain D: D.2, F.3, N.5, N.154 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.2 Water bridges: D:N.154

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: N.65, W.357 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:K.383 Hydrogen bonds: A:N.65, A:W.357 NAG.9: 2 residues within 4Å: Chain B: N.65, W.357 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Water bridges: D:K.383 Hydrogen bonds: B:N.65, B:W.357 NAG.15: 2 residues within 4Å: Chain C: N.65, W.357 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Water bridges: B:K.383 Hydrogen bonds: C:N.65, C:W.357 NAG.21: 2 residues within 4Å: Chain D: N.65, W.357 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.65, D:W.357 Water bridges: A:K.383

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 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.4 CA.5: 3 residues within 4Å: Ligands: CA.11, CA.17, CA.23 No protein-ligand interaction detected (PLIP) CA.10: 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.15, H2O.18 CA.11: 3 residues within 4Å: Ligands: CA.5, CA.17, CA.23 No protein-ligand interaction detected (PLIP) CA.16: 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.29, H2O.32 CA.17: 3 residues within 4Å: Ligands: CA.5, CA.11, CA.23 No protein-ligand interaction detected (PLIP) CA.22: 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.43, H2O.46 CA.23: 3 residues within 4Å: Ligands: CA.5, CA.11, CA.17 No protein-ligand interaction detected (PLIP)

4 x 4AM: 4-AMINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID(Non-covalent)

4AM.6: 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:R.71, A:R.144, A:E.197, A:R.212 Water bridges: A:R.75, A:R.75, A:R.144, A:E.197, A:E.197, A:E.197 Salt bridges: A:R.37, A:R.212, A:R.290 4AM.12: 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:R.71, B:R.144, B:E.197, B:R.212 Water bridges: B:R.75, B:R.75, B:R.144, B:E.197, B:E.197, B:E.197 Salt bridges: B:R.37, B:R.212, B:R.290 4AM.18: 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:R.71, C:R.144, C:E.197, C:R.212 Water bridges: C:R.75, C:R.75, C:R.144, C:E.197, C:E.197, C:E.197 Salt bridges: C:R.37, C:R.212, C:R.290 4AM.24: 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:R.71, D:R.144, D:E.197, D:R.212 Water bridges: D:R.75, D:R.75, D:R.144, D:E.197, D:E.197, D:E.197 Salt bridges: D:R.37, D:R.212, D:R.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, B.J. et al., Analysis of inhibitor binding in influenza virus neuraminidase. Protein Sci. (2001)

Release Date

2001-04-11

Peptides

NEURAMINIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

NEURAMINIDASE

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