SMTL ID : 8jgr.1

Crystal structure of Deinococcus radiodurans exopolyphosphatase in the presence of Pi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 12 residues within 4Å: Chain A: G.29, T.30, T.102, S.103, R.106, E.134, G.158, G.159, G.160, S.161 Ligands: PO4.2, K.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.30, A:T.30, A:T.30, A:T.102, A:T.102, A:T.102, A:S.103, A:R.106, A:G.160, A:S.161 PO4.2: 8 residues within 4Å: Chain A: G.29, T.30, N.31, S.32, G.158, G.159 Ligands: PO4.1, PO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.30, A:N.31, A:N.31, A:S.32, A:G.159 PO4.3: 7 residues within 4Å: Chain A: N.31, S.32, H.34, G.233, R.291 Ligands: PO4.2, PO4.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.31, A:S.32, A:G.233 Salt bridges: A:H.34, A:R.291 PO4.4: 5 residues within 4Å: Chain A: H.34, G.233, E.236, R.291 Ligands: PO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.291 Salt bridges: A:H.34

2 x K: POTASSIUM ION(Non-covalent)

K.5: 1 residues within 4Å: Chain A: R.210 No protein-ligand interaction detected (PLIP) K.6: 5 residues within 4Å: Chain A: E.134, D.156, G.158, E.163 Ligands: PO4.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.134, A:D.156, A:E.163

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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