SMTL ID : 2qwk.1

THE X-RAY STRUCTURE OF A COMPLEX OF 5-N-ACETYL-5-AMINO-3-(1-ETHYLPROPOXY)-1-CYCLOHEXENE-1-CARBOXYLIC ACID (GS4071) AND WILDTYPE TERN N9 INFLUENZA VIRUS NEURAMINIDASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 20 residues within 4Å: Chain A: N.119, N.120, R.140 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 6 PLIP interactions: 6 interactions with chain B Water bridges: B:Q.313, B:Q.311, B:G.312 Hydrophobic interactions: B:F.372 Hydrogen bonds: B:G.312, B:G.312, B:Q.375 NAG-NAG-BMA-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 6 PLIP interactions: 6 interactions with chain D Water bridges: D:Q.313, D:Q.311, D:G.312 Hydrophobic interactions: D:F.372 Hydrogen bonds: D:G.312, D:G.312, D:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.13: 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 C: N.119, N.120, R.140 6 PLIP interactions: 6 interactions with chain A Water bridges: A:Q.313, A:Q.311, A:G.312 Hydrophobic interactions: A:F.372 Hydrogen bonds: A:G.312, A:G.312, A:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 20 residues within 4Å: 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 Chain D: N.119, N.120, R.140 6 PLIP interactions: 6 interactions with chain C Water bridges: C:Q.313, C:Q.311, C:G.312 Hydrophobic interactions: C:F.372 Hydrogen bonds: C:G.312, C:G.312, C:Q.375

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 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: D.2, F.3, N.5, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: D.2, F.3, N.5, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain D: D.2, F.3, N.5, N.154 No protein-ligand interaction detected (PLIP)

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65, A:W.357 NAG.9: 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.15: 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.21: 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 G39: (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid(Non-covalent)

G39.4: 13 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, W.98, I.142, R.144, E.196, E.197, R.212, N.214, R.290, Y.324 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.98 Hydrogen bonds: A:E.38, A:R.71 Water bridges: A:R.37, A:R.75 Salt bridges: A:R.37, A:R.212, A:R.290 G39.10: 13 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, W.98, I.142, R.144, E.196, E.197, R.212, N.214, R.290, Y.324 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.98 Hydrogen bonds: B:E.38, B:R.71 Water bridges: B:R.37, B:R.75 Salt bridges: B:R.37, B:R.212, B:R.290 G39.16: 13 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.98, I.142, R.144, E.196, E.197, R.212, N.214, R.290, Y.324 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.98 Hydrogen bonds: C:E.38, C:R.71 Water bridges: C:R.37, C:R.75 Salt bridges: C:R.37, C:R.212, C:R.290 G39.22: 13 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, W.98, I.142, R.144, E.196, E.197, R.212, N.214, R.290, Y.324 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.98 Hydrogen bonds: D:E.38, D:R.71 Water bridges: D:R.37, D:R.75 Salt bridges: D:R.37, D:R.212, D:R.290

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

CA.5: 4 residues within 4Å: Chain A: D.213, G.217, D.244, N.266 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.244, A:N.266, H2O.1, H2O.4 CA.6: 3 residues within 4Å: Ligands: CA.12, CA.18, CA.24 No protein-ligand interaction detected (PLIP) CA.11: 4 residues within 4Å: Chain B: D.213, G.217, D.244, N.266 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.244, B:N.266, H2O.14, H2O.17 CA.12: 3 residues within 4Å: Ligands: CA.6, CA.18, CA.24 No protein-ligand interaction detected (PLIP) CA.17: 4 residues within 4Å: Chain C: D.213, G.217, D.244, N.266 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.244, C:N.266, H2O.28, H2O.31 CA.18: 3 residues within 4Å: Ligands: CA.6, CA.12, CA.24 No protein-ligand interaction detected (PLIP) CA.23: 4 residues within 4Å: Chain D: D.213, G.217, D.244, N.266 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.244, D:N.266, H2O.41, H2O.44 CA.24: 3 residues within 4Å: Ligands: CA.6, CA.12, CA.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varghese, J.N. et al., Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase. Structure (1998)

Release Date

1998-11-11

Peptides

NEURAMINIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

NEURAMINIDASE

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