SMTL ID : 2qwf.1

THE X-RAY STRUCTURE OF A COMPLEX OF N-ACETYL-4-GUANIDINO-6-METHYL(PROPYL)CARBOXAMIDE-4,5-DIHYDRO-2H-PYRAN-2-CARBOXYLIC ACID AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: 19 residues within 4Å: Chain A: N.119, N.120 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 5 PLIP interactions: 5 interactions with chain B Water bridges: B:G.312, B:Q.311, B:G.312 Hydrophobic interactions: B:F.372 Hydrogen bonds: B:G.312, B:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.7: 19 residues within 4Å: Chain B: N.119, N.120 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 Water bridges: D:G.312, D:Q.311, D:G.312 Hydrophobic interactions: D:F.372 Hydrogen bonds: D:G.312, D:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.13: 19 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 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.312, A:Q.311, A:G.312 Hydrophobic interactions: A:F.372 Hydrogen bonds: A:G.312, A:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 19 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 5 PLIP interactions: 5 interactions with chain C Water bridges: C:G.312, C:Q.311, C:G.312 Hydrophobic interactions: C:F.372 Hydrogen bonds: 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 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.65, A:W.357 Water bridges: B:K.383 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 A, 2 interactions with chain C Water bridges: A: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 C Hydrogen bonds: D:N.65, D:W.357 Water bridges: C:K.383

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

CA.4: 5 residues within 4Å: Chain A: D.213, N.214, 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.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, N.214, 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.16, H2O.19 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, N.214, 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.31, H2O.35 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, N.214, 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.47, H2O.50 CA.23: 3 residues within 4Å: Ligands: CA.5, CA.11, CA.17 No protein-ligand interaction detected (PLIP)

4 x G20: 5-N-acetyl-4-guanidino-6-methyl(propyl) carboxamide-4,5-dihydro-2H-pyran-2-carboxylic acid(Non-covalent)

G20.6: 15 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, K.212, R.290, Y.324 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142, A:I.142, A:R.144, A:A.166 Hydrogen bonds: A:R.71, A:W.98, A:W.98 Water bridges: A:R.75, A:R.75, A:E.147, A:E.147, A:K.212, A:Y.324, A:Y.324 Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.290 G20.12: 15 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, K.212, R.290, Y.324 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142, B:I.142, B:R.144, B:A.166 Hydrogen bonds: B:R.71, B:W.98, B:W.98 Water bridges: B:R.75, B:R.75, B:E.147, B:E.147, B:K.212, B:Y.324, B:Y.324 Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.290 G20.18: 15 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, K.212, R.290, Y.324 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:I.142, C:R.144, C:A.166 Hydrogen bonds: C:R.71, C:W.98, C:W.98 Water bridges: C:R.75, C:R.75, C:E.147, C:E.147, C:K.212, C:Y.324, C:Y.324 Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.290 G20.24: 15 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, K.212, R.290, Y.324 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:I.142, D:R.144, D:A.166 Hydrogen bonds: D:R.71, D:W.98, D:W.98 Water bridges: D:R.75, D:R.75, D:E.147, D:E.147, D:K.212, D:Y.324, D:Y.324 Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.290

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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