SMTL ID : 3x0o.1

ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESMM-state at reaction time of 10 min

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.09 Å

Oligo State

homo-dimer

Ligands

2 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.1: 20 residues within 4Å: Chain A: I.19, A.36, R.54, E.63, A.66, G.67, L.68, E.82, E.86, E.108 Chain B: R.27, Y.28, E.29, I.30, S.102, P.103, G.104, F.105 Ligands: MN.4, MN.5 22 PLIP interactions: 15 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:L.68, A:E.108, B:E.29, B:E.29, B:S.102, B:G.104, B:F.105 Water bridges: A:Q.52, A:R.54, A:R.54, A:R.54, A:R.54, A:R.54, A:R.54, A:R.54, A:A.66, A:R.81, A:T.110 Salt bridges: A:R.54, A:R.54 pi-Stacking: B:Y.28, B:Y.28 AR6.6: 20 residues within 4Å: Chain A: R.27, Y.28, E.29, I.30, S.102, P.103, G.104, F.105 Chain B: I.19, A.36, R.54, E.63, A.66, G.67, L.68, E.82, E.86, E.108 Ligands: MN.9, MN.10 22 PLIP interactions: 7 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:E.29, A:E.29, A:S.102, A:G.104, A:F.105, B:L.68, B:E.108 pi-Stacking: A:Y.28, A:Y.28 Water bridges: B:Q.52, B:R.54, B:R.54, B:R.54, B:R.54, B:R.54, B:R.54, B:R.54, B:E.63, B:A.66, B:R.81 Salt bridges: B:R.54, B:R.54

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: G.17, R.18, I.19, L.20, N.21, E.32, H.33, K.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.17 Water bridges: A:H.33, A:H.33 GOL.7: 8 residues within 4Å: Chain B: G.17, R.18, I.19, L.20, N.21, E.32, H.33, K.34 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.17 Water bridges: B:H.33, B:H.33

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

SO4.3: 3 residues within 4Å: Chain A: R.51, R.144, E.149 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.51, A:R.51 Salt bridges: A:R.51, A:R.144 SO4.8: 3 residues within 4Å: Chain B: R.51, R.144, E.149 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.51 Salt bridges: B:R.51, B:R.144

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

MN.4: 4 residues within 4Å: Chain A: A.66, E.86 Ligands: AR6.1, MN.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.66, A:E.86, H2O.1, H2O.1, H2O.5 MN.5: 4 residues within 4Å: Chain A: E.82, E.86 Ligands: AR6.1, MN.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.82, A:E.86, H2O.1, H2O.5 MN.9: 4 residues within 4Å: Chain B: A.66, E.86 Ligands: AR6.6, MN.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.66, B:E.86, H2O.6, H2O.6, H2O.10 MN.10: 4 residues within 4Å: Chain B: E.82, E.86 Ligands: AR6.6, MN.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.82, B:E.86, H2O.6, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furuike, Y. et al., ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors. Biochemistry (2016)

Release Date

2016-04-27

Peptides

ADP-ribose pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ADP-ribose pyrophosphatase

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