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

2009 H1N1 PA endonuclease mutant E119D in complex with dTMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.61, D.109, D.120, I.121 Ligands: TMP.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:D.120, A:I.121 MN.4: 5 residues within 4Å: Chain B: H.61, D.109, D.120, I.121 Ligands: TMP.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:D.120, B:I.121 MN.7: 5 residues within 4Å: Chain C: H.61, D.109, D.120, I.121 Ligands: TMP.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:D.120, C:I.121 MN.10: 5 residues within 4Å: Chain D: H.61, D.109, D.120, I.121 Ligands: TMP.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:D.120, D:I.121

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

SO4.2: 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: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 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.51, B:E.51, B:T.52, B:N.53, B:N.53, B:K.54, B:S.195 SO4.8: 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:E.51, C:T.52, C:N.53, C:N.53, C:K.54, C:S.195 SO4.11: 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:E.51, D:T.52, D:N.53, D:N.53, D:K.54, D:S.195

4 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.3: 13 residues within 4Å: Chain A: K.54, A.57, I.58, H.61, D.120, I.121, G.122, V.123, R.125, Y.131, K.135, E.196 Ligands: MN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.61, A:Y.131 Hydrogen bonds: A:Y.44, A:Y.44, A:V.123, A:R.125 Water bridges: A:Y.131 Salt bridges: A:H.61, A:K.135 TMP.6: 13 residues within 4Å: Chain B: K.54, A.57, I.58, H.61, D.120, I.121, G.122, V.123, R.125, Y.131, K.135, E.196 Ligands: MN.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.61, B:Y.131 Hydrogen bonds: B:Y.44, B:Y.44, B:V.123, B:R.125 Water bridges: B:Y.131 Salt bridges: B:H.61, B:K.135 TMP.9: 13 residues within 4Å: Chain C: K.54, A.57, I.58, H.61, D.120, I.121, G.122, V.123, R.125, Y.131, K.135, E.196 Ligands: MN.7 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:H.61, C:Y.131 Hydrogen bonds: C:Y.44, C:Y.44, C:V.123, C:R.125 Water bridges: C:Y.131 Salt bridges: C:H.61, C:K.135 TMP.12: 13 residues within 4Å: Chain D: K.54, A.57, I.58, H.61, D.120, I.121, G.122, V.123, R.125, Y.131, K.135, E.196 Ligands: MN.10 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:H.61, D:Y.131 Hydrogen bonds: D:Y.44, D:Y.44, D:V.123, D:R.125 Water bridges: D:Y.131 Salt bridges: D:H.61, D:K.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, M.S. et al., Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor. Proc. Natl. Acad. Sci. U.S.A. (2016)

Release Date

2016-03-23

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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