SMTL ID : 5vrj.2 (1 other biounit)

2009 H1N1 PA Endonuclease in complex with RO-7 and Magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 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 SO4.5: 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 SO4.9: 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 SO4.13: 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

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: H.61, D.109, E.120, I.121, K.135 Ligands: MG.3, R07.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MG.3: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: MG.2, R07.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.81, A:D.109, H2O.1, H2O.1 MG.6: 7 residues within 4Å: Chain B: H.61, D.109, E.120, I.121, K.135 Ligands: MG.7, R07.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MG.7: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: MG.6, R07.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.81, B:D.109, H2O.1, H2O.1 MG.10: 7 residues within 4Å: Chain C: H.61, D.109, E.120, I.121, K.135 Ligands: MG.11, R07.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MG.11: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: MG.10, R07.12 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.1, H2O.1 MG.14: 7 residues within 4Å: Chain D: H.61, D.109, E.120, I.121, K.135 Ligands: MG.15, R07.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MG.15: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MG.14, R07.16 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.1, H2O.1

4 x R07: 1-[(11S)-6,11-dihydrodibenzo[b,e]thiepin-11-yl]-5-hydroxy-3-[(2R)-1,1,1-trifluoropropan-2-yl]-2,3-dihydro-1H-pyrido[2,1-f][1,2,4]triazine-4,6-dione(Non-covalent)

R07.4: 15 residues within 4Å: Chain A: A.40, Y.44, E.46, A.57, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131, K.135 Ligands: MG.2, MG.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.40, A:Y.44, A:Y.44, A:I.58, A:I.58, A:H.61 Hydrogen bonds: A:K.135 pi-Stacking: A:H.61 Halogen bonds: A:L.107 R07.8: 15 residues within 4Å: Chain B: A.40, Y.44, E.46, A.57, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131, K.135 Ligands: MG.6, MG.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.40, B:Y.44, B:Y.44, B:I.58, B:I.58, B:H.61 Hydrogen bonds: B:K.135 pi-Stacking: B:H.61 Halogen bonds: B:L.107 R07.12: 15 residues within 4Å: Chain C: A.40, Y.44, E.46, A.57, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131, K.135 Ligands: MG.10, MG.11 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.40, C:Y.44, C:Y.44, C:I.58, C:I.58, C:H.61 Hydrogen bonds: C:K.135 pi-Stacking: C:H.61 Halogen bonds: C:L.107 R07.16: 15 residues within 4Å: Chain D: A.40, Y.44, E.46, A.57, I.58, H.61, E.81, L.107, D.109, E.120, I.121, Y.131, K.135 Ligands: MG.14, MG.15 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:A.40, D:Y.44, D:Y.44, D:I.58, D:I.58, D:H.61 Hydrogen bonds: D:E.81, D:D.109, D:K.135 pi-Stacking: D:H.61 Halogen bonds: D:L.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, J.C. et al., Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. MBio (2018)

Release Date

2018-04-11

Peptides

Polymerase acidic protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Polymerase acidic protein

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