SMTL ID : 7rkp.1

The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with cyclic compound SJ001034733

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-tetramer

Ligands

4 x QQ4: Hexa Vinylpyrrolidone K15(Non-covalent)

QQ4.1: 5 residues within 4Å: Chain A: M.32, F.66, I.79, E.81, G.82 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.66, A:F.66, A:F.66, A:I.79 Hydrogen bonds: A:N.30 QQ4.8: 5 residues within 4Å: Chain B: M.32, F.66, I.79, E.81, G.82 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.66, B:F.66, B:F.66, B:I.79 Hydrogen bonds: B:N.30 QQ4.15: 5 residues within 4Å: Chain C: M.32, F.66, I.79, E.81, G.82 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66, C:F.66, C:I.79 Hydrogen bonds: C:N.30 QQ4.22: 5 residues within 4Å: Chain D: M.32, F.66, I.79, E.81, G.82 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.66, D:F.66, D:F.66, D:I.79 Hydrogen bonds: D:N.30

4 x 5Y1: (5R)-5-hydroxy-16,21-dioxa-3,8,28-triazatetracyclo[20.3.1.1~2,6~.1~11,15~]octacosa-1(26),2,6(28),11(27),12,14,22,24-octaene-4,7-dione(Non-covalent)

5Y1.2: 11 residues within 4Å: Chain A: Y.44, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.3, MN.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.44, A:K.54 Hydrogen bonds: A:Y.131, A:K.135 pi-Stacking: A:Y.44, A:H.61 5Y1.9: 11 residues within 4Å: Chain B: Y.44, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.10, MN.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.44, B:K.54 Hydrogen bonds: B:Y.131, B:K.135 pi-Stacking: B:Y.44, B:H.61 5Y1.16: 11 residues within 4Å: Chain C: Y.44, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.17, MN.18 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.44, C:K.54 Hydrogen bonds: C:Y.131, C:K.135 pi-Stacking: C:Y.44, C:H.61 5Y1.23: 11 residues within 4Å: Chain D: Y.44, K.54, H.61, E.81, D.109, E.120, I.121, Y.131, K.135 Ligands: MN.24, MN.25 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.44, D:K.54 Hydrogen bonds: D:Y.131, D:K.135 pi-Stacking: D:Y.44, D:H.61

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

MN.3: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: 5Y1.2, MN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MN.4: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: 5Y1.2, MN.3 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.10: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: 5Y1.9, MN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.11: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: 5Y1.9, MN.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.17: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: 5Y1.16, MN.18 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.18: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: 5Y1.16, MN.17 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.1, H2O.1 MN.24: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: 5Y1.23, MN.25 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.25: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: 5Y1.23, MN.24 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.1, H2O.1

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

SO4.5: 4 residues within 4Å: Chain A: Y.44, R.85, W.89, L.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.44, A:W.89 Salt bridges: A:R.85 SO4.6: 3 residues within 4Å: Chain A: G.72, S.73, R.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.73 Salt bridges: A:R.76 SO4.7: 6 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54, S.195 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.51, A:T.52, A:N.53, A:N.53, A:N.53, A:K.54, A:S.195 SO4.12: 4 residues within 4Å: Chain B: Y.44, R.85, W.89, L.107 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.44, B:W.89 Salt bridges: B:R.85 SO4.13: 3 residues within 4Å: Chain B: G.72, S.73, R.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.73 Salt bridges: B:R.76 SO4.14: 6 residues within 4Å: Chain B: I.50, E.51, T.52, N.53, K.54, S.195 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.51, B:T.52, B:N.53, B:N.53, B:N.53, B:K.54, B:S.195 SO4.19: 4 residues within 4Å: Chain C: Y.44, R.85, W.89, L.107 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.44, C:W.89 Salt bridges: C:R.85 SO4.20: 3 residues within 4Å: Chain C: G.72, S.73, R.76 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.73 Salt bridges: C:R.76 SO4.21: 6 residues within 4Å: Chain C: I.50, E.51, T.52, N.53, K.54, S.195 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.51, C:T.52, C:N.53, C:N.53, C:N.53, C:K.54, C:S.195 SO4.26: 4 residues within 4Å: Chain D: Y.44, R.85, W.89, L.107 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.44, D:W.89 Salt bridges: D:R.85 SO4.27: 3 residues within 4Å: Chain D: G.72, S.73, R.76 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.73 Salt bridges: D:R.76 SO4.28: 6 residues within 4Å: Chain D: I.50, E.51, T.52, N.53, K.54, S.195 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.51, D:T.52, D:N.53, D:N.53, D:N.53, D:K.54, D:S.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Slavish, P.J. et al., Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential. Eur.J.Med.Chem. (2023)

Release Date

2022-07-27

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