SMTL ID : 8jgw.1

Crystal structure of Klebsiella pneumoniae exopolyphosphatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: S.497, Q.498, N.499, A.500 Chain B: S.90, E.94 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.90, A:S.497, A:A.500 Water bridges: B:Q.97 GOL.2: 7 residues within 4Å: Chain A: G.59, R.60, L.61, R.95 Chain B: N.467, Q.468, D.505 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.467, B:N.467, B:D.505, A:R.60, A:R.60, A:R.95 Water bridges: B:Q.468 GOL.10: 6 residues within 4Å: Chain A: N.467, D.505 Chain B: G.59, R.60, L.61, R.95 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.60, A:N.467, A:D.505 Water bridges: B:R.95, A:N.467

8 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: Q.468, A.471, T.473 Chain B: E.94, Q.97 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.94, A:A.471, H2O.13 K.4: 5 residues within 4Å: Chain A: E.94, Q.97 Chain B: Q.468, A.471, T.473 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.94, B:A.471, H2O.2 K.5: 4 residues within 4Å: Chain A: A.471, T.472, T.473 Chain B: Q.97 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.471, H2O.9, H2O.10 K.6: 4 residues within 4Å: Chain A: W.230, I.307, K.308, E.309 No protein-ligand interaction detected (PLIP) K.7: 3 residues within 4Å: Chain A: R.185, R.186, K.217 No protein-ligand interaction detected (PLIP) K.8: 6 residues within 4Å: Chain A: H.110, E.141, D.163, G.165, S.168, E.170 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.163, A:E.170 K.11: 3 residues within 4Å: Chain B: W.230, I.307, K.308 No protein-ligand interaction detected (PLIP) K.12: 4 residues within 4Å: Chain A: Q.97 Chain B: A.471, T.472, T.473 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.471, H2O.19

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain A: L.414, F.417, Q.422 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.414, A:F.417, H2O.1, H2O.6

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Exopolyphosphatase