SMTL ID : 5wb3.1 (1 other biounit)

Crystal structure of the influenza virus PA endonuclease in complex with inhibitor 10j (SRI-30026)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: MN.2, GYA.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MN.2: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: MN.1, GYA.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.81, A:D.109, H2O.1, H2O.1 MN.6: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: MN.7, GYA.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.7: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: MN.6, GYA.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.81, B:D.109, H2O.1, H2O.1 MN.11: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.12, GYA.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.12: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: MN.11, GYA.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.2, H2O.2 MN.16: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.17, GYA.20 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.17: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MN.16, GYA.20 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.2, H2O.3

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.73 Salt bridges: A:R.76, A:K.114 SO4.4: 6 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.51, A:T.52, A:N.53, A:N.53, A:K.54, A:S.195 SO4.8: 4 residues within 4Å: Chain B: G.72, S.73, R.76, K.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.73 Salt bridges: B:R.76, B:K.114 SO4.9: 6 residues within 4Å: Chain B: I.50, E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.51, B:T.52, B:N.53, B:N.53, B:K.54, B:S.195 SO4.13: 4 residues within 4Å: Chain C: G.72, S.73, R.76, K.114 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.73 Salt bridges: C:R.76, C:K.114 SO4.14: 6 residues within 4Å: Chain C: I.50, E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.51, C:T.52, C:N.53, C:N.53, C:K.54, C:S.195 SO4.18: 4 residues within 4Å: Chain D: G.72, S.73, R.76, K.114 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.73 Salt bridges: D:R.76, D:K.114 SO4.19: 6 residues within 4Å: Chain D: I.50, E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.51, D:T.52, D:N.53, D:N.53, D:K.54, D:S.195

4 x GYA: 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-(5,6-dimethoxy-2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-ox o-1,6-dihydropyrimidine-4-carboxamide(Non-covalent)

GYA.5: 12 residues within 4Å: Chain A: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121 Ligands: MN.1, MN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.40, A:Y.44, A:Y.44, A:Y.44, A:I.58 Hydrogen bonds: A:K.54 Water bridges: A:I.121, A:Y.131 GYA.10: 12 residues within 4Å: Chain B: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121 Ligands: MN.6, MN.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.40, B:Y.44, B:Y.44, B:Y.44, B:I.58 Hydrogen bonds: B:K.54 Water bridges: B:I.121, B:Y.131 GYA.15: 12 residues within 4Å: Chain C: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121 Ligands: MN.11, MN.12 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.40, C:Y.44, C:Y.44, C:Y.44, C:I.58 Hydrogen bonds: C:K.54 Water bridges: C:I.121, C:Y.131 GYA.20: 12 residues within 4Å: Chain D: A.40, Y.44, E.46, K.54, I.58, H.61, E.81, D.109, E.120, I.121 Ligands: MN.16, MN.17 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.40, D:Y.44, D:Y.44, D:Y.44, D:I.58 Hydrogen bonds: D:K.54 Water bridges: D:I.121, D:Y.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beylkin, D. et al., Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease. Sci Rep (2017)

Release Date

2018-01-03

Peptides

Polymerase acidic protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Polymerase acidic protein

Related Entries With Identical Sequence