SMTL ID : 8jgq.1

Crystal structure of Deinococcus radiodurans exopolyphosphatase complexed with P5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x UG3: bis[oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate(Non-covalent)

UG3.1: 21 residues within 4Å: Chain A: D.27, G.29, T.30, N.31, S.32, H.34, K.55, R.57, T.102, S.103, E.134, D.156, L.157, G.158, G.159, G.160, S.161, S.232, G.233, T.234, R.291 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:D.27, A:T.30, A:T.30, A:T.30, A:T.30, A:N.31, A:N.31, A:S.32, A:S.32, A:T.102, A:S.103, A:E.134, A:L.157, A:G.159, A:G.160, A:S.161, A:S.232, A:G.233, A:T.234 Water bridges: A:D.156, A:G.158 Salt bridges: A:H.34, A:H.34, A:K.55, A:R.57, A:R.291, A:R.291

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

SO4.2: 4 residues within 4Å: Chain A: S.341, R.343, Q.344, S.388 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.341, A:S.341, A:Q.344, A:S.388 Water bridges: A:R.369, A:R.369 Salt bridges: A:R.343 SO4.3: 1 residues within 4Å: Chain A: R.284 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.284 SO4.4: 3 residues within 4Å: Chain A: G.259, E.260, R.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.246, A:R.261 Salt bridges: A:R.261 SO4.5: 3 residues within 4Å: Chain A: R.343, P.385, D.428 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.428 Salt bridges: A:R.343 SO4.6: 2 residues within 4Å: Chain A: R.119, R.477 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.119, A:R.477 SO4.7: 4 residues within 4Å: Chain A: T.53, L.54, K.55, R.322 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.53, A:L.54, A:K.55 Salt bridges: A:R.322

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: H.360, H.397, E.398, D.473 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.360, A:H.397, A:E.398, A:D.473, A:D.473

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, S. et al., Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling. Adv Sci (2024)

Release Date

2024-05-15

Peptides

Exopolyphosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Exopolyphosphatase

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