SMTL ID : 2yz5.1

Histidinol Phosphate Phosphatase complexed with Phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.13, H.38, H.226 Ligands: PO4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.13, A:H.38, A:H.226 ZN.7: 4 residues within 4Å: Chain B: H.13, H.38, H.226 Ligands: PO4.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.13, B:H.38, B:H.226 ZN.10: 4 residues within 4Å: Chain C: H.13, H.38, H.226 Ligands: PO4.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.13, C:H.38, C:H.226 ZN.16: 4 residues within 4Å: Chain D: H.13, H.38, H.226 Ligands: PO4.18 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.13, D:H.38, D:H.226

8 x FE: FE (III) ION(Non-covalent)

FE.2: 5 residues within 4Å: Chain A: E.80, H.108, H.154 Ligands: FE.3, PO4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.80, A:H.108, A:H.154, H2O.6 FE.3: 6 residues within 4Å: Chain A: H.5, H.7, E.80, D.224 Ligands: FE.2, PO4.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.5, A:H.7, A:E.80, A:D.224, H2O.6 FE.6: 5 residues within 4Å: Chain B: E.80, H.108, H.154 Ligands: FE.8, PO4.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.80, B:H.108, B:H.154, H2O.12 FE.8: 6 residues within 4Å: Chain B: H.5, H.7, E.80, D.224 Ligands: FE.6, PO4.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.5, B:H.7, B:E.80, B:D.224, H2O.12 FE.11: 5 residues within 4Å: Chain C: E.80, H.108, H.154 Ligands: FE.12, PO4.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.80, C:H.108, C:H.154, H2O.18 FE.12: 6 residues within 4Å: Chain C: H.5, H.7, E.80, D.224 Ligands: FE.11, PO4.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.5, C:H.7, C:E.80, C:D.224, H2O.18 FE.15: 5 residues within 4Å: Chain D: E.80, H.108, H.154 Ligands: FE.17, PO4.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.80, D:H.108, D:H.154, H2O.23 FE.17: 6 residues within 4Å: Chain D: H.5, H.7, E.80, D.224 Ligands: FE.15, PO4.18 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.5, D:H.7, D:E.80, D:D.224, H2O.23

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

PO4.4: 11 residues within 4Å: Chain A: H.7, H.13, H.38, E.80, H.108, D.116, D.224, H.226 Ligands: ZN.1, FE.2, FE.3 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.191 Salt bridges: A:H.7, A:H.38, A:H.108, A:H.226 PO4.9: 11 residues within 4Å: Chain B: H.7, H.13, H.38, E.80, H.108, D.116, D.224, H.226 Ligands: FE.6, ZN.7, FE.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.224 Water bridges: B:D.116, B:N.191 Salt bridges: B:H.7, B:H.38, B:H.108, B:H.226 PO4.13: 11 residues within 4Å: Chain C: H.7, H.13, H.38, E.80, H.108, D.116, D.224, H.226 Ligands: ZN.10, FE.11, FE.12 5 PLIP interactions: 5 interactions with chain C Water bridges: C:N.191 Salt bridges: C:H.7, C:H.38, C:H.108, C:H.226 PO4.18: 11 residues within 4Å: Chain D: H.7, H.13, H.38, E.80, H.108, D.116, D.224, H.226 Ligands: FE.15, ZN.16, FE.17 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.80, D:D.224 Water bridges: D:D.116, D:N.191 Salt bridges: D:H.7, D:H.38, D:H.108, D:H.226

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: L.10, C.11, G.12, P.47, E.48, R.50, R.52 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.9 Water bridges: A:G.12, A:P.47, A:R.50, A:R.52 GOL.14: 7 residues within 4Å: Chain C: L.10, C.11, G.12, P.47, E.48, R.50, R.52 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.9 Water bridges: C:G.12, C:P.47, C:R.50, C:R.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Omi, R. et al., Crystal Structure of Monofunctional Histidinol Phosphate Phosphatase from Thermus thermophilus HB8. Biochemistry (2007)

Release Date

2007-11-27

Peptides

Histidinol phosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Histidinol phosphatase

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