SMTL ID : 2qwi.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 WILDTYPE TERN N9 INFLUENZA VIRUS NEURAMINIDASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.1: 21 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 Ligands: MAN.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.310, B:R.247, B:D.250, B:I.285, B:G.312, B:G.312, B:Q.375 Water bridges: B:G.312, B:Q.313, B:R.247, B:P.248, B:D.250 Hydrophobic interactions: B:F.372 NAG-NAG-BMA-MAN-MAN-MAN.7: 21 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 Ligands: MAN.8 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.310, D:R.247, D:D.250, D:I.285, D:G.312, D:G.312, D:Q.375 Water bridges: D:G.312, D:Q.313, D:R.247, D:P.248, D:D.250 Hydrophobic interactions: D:F.372 NAG-NAG-BMA-MAN-MAN-MAN.13: 21 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 Ligands: MAN.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.310, A:R.247, A:D.250, A:I.285, A:G.312, A:G.312, A:Q.375 Water bridges: A:G.312, A:Q.313, A:R.247, A:P.248, A:D.250 Hydrophobic interactions: A:F.372 NAG-NAG-BMA-MAN-MAN-MAN.19: 21 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 Ligands: MAN.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.310, C:R.247, C:D.250, C:I.285, C:G.312, C:G.312, C:Q.375 Water bridges: C:G.312, C:Q.313, C:R.247, C:P.248, C:D.250 Hydrophobic interactions: C:F.372

4 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.2: 3 residues within 4Å: Chain B: P.309, T.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) MAN.8: 3 residues within 4Å: Chain D: P.309, T.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) MAN.14: 3 residues within 4Å: Chain A: P.309, T.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.13 No protein-ligand interaction detected (PLIP) MAN.20: 3 residues within 4Å: Chain C: P.309, T.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.19 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.3 Water bridges: A:N.5, A:N.5 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.9: 4 residues within 4Å: Chain B: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.3 Water bridges: B:N.5, B:N.5 NAG.10: 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: 4 residues within 4Å: Chain C: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.3 Water bridges: C:N.5, C:N.5 NAG.16: 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: 4 residues within 4Å: Chain D: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.3 Water bridges: D:N.5, D:N.5 NAG.22: 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 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.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.8, H2O.12 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.16, H2O.19 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.23, H2O.27

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, R.212, R.290, Y.324 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142, A:R.144, A:A.166 Hydrogen bonds: A:R.71, A:W.98, A:W.98, A:Y.324 Water bridges: A:R.75, A:R.75, A:E.147, A:E.147 Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.212, 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, R.212, R.290, Y.324 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142, B:R.144, B:A.166 Hydrogen bonds: B:R.71, B:W.98, B:W.98, B:Y.324 Water bridges: B:R.75, B:R.75, B:E.147, B:E.147 Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.212, 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, R.212, R.290, Y.324 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:R.144, C:A.166 Hydrogen bonds: C:R.71, C:W.98, C:W.98, C:Y.324 Water bridges: C:R.75, C:R.75, C:E.147, C:E.147 Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.212, 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, R.212, R.290, Y.324 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:R.144, D:A.166 Hydrogen bonds: D:R.71, D:W.98, D:W.98, D:Y.324 Water bridges: D:R.75, D:R.75, D:E.147, D:E.147 Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.212, 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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