SMTL ID : 3g3q.3 (2 other biounits)

Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate polymer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 4 residues within 4Å: Ligands: PO4.2, PO4.28, PO4.29, PO4.30 Ligand excluded by PLIP PO4.2: 4 residues within 4Å: Chain A: K.270 Ligands: PO4.1, PO4.3, PO4.30 Ligand excluded by PLIP PO4.3: 5 residues within 4Å: Chain A: K.270 Ligands: PO4.2, PO4.4, PO4.5, PO4.30 Ligand excluded by PLIP PO4.4: 6 residues within 4Å: Chain A: H.98, S.107, K.270 Ligands: PO4.3, PO4.5, PO4.6 Ligand excluded by PLIP PO4.5: 9 residues within 4Å: Chain A: R.68, K.71, H.98, S.107, K.270 Ligands: PO4.3, PO4.4, PO4.6, PO4.7 Ligand excluded by PLIP PO4.6: 7 residues within 4Å: Chain A: K.15, K.96, K.270 Ligands: PO4.4, PO4.5, PO4.7, PO4.12 Ligand excluded by PLIP PO4.7: 10 residues within 4Å: Chain A: K.15, R.68, K.71, K.96, F.271, S.272 Ligands: PO4.5, PO4.6, PO4.8, PO4.9 Ligand excluded by PLIP PO4.8: 9 residues within 4Å: Chain A: Y.56, R.68, R.79, K.96, S.272, F.274 Ligands: PO4.7, PO4.9, PO4.10 Ligand excluded by PLIP PO4.9: 9 residues within 4Å: Chain A: K.15, Y.56, F.271, S.272, K.273 Ligands: PO4.7, PO4.8, PO4.10, PO4.11 Ligand excluded by PLIP PO4.10: 9 residues within 4Å: Chain A: Y.56, R.79, R.81, Y.174, R.176, K.273 Ligands: PO4.8, PO4.9, PO4.11 Ligand excluded by PLIP PO4.11: 9 residues within 4Å: Chain A: R.79, R.81, K.96, K.109, Y.174, R.176 Ligands: PO4.9, PO4.10, PO4.12 Ligand excluded by PLIP PO4.12: 8 residues within 4Å: Chain A: K.96, K.109, R.176, E.241, K.243 Ligands: PO4.6, PO4.11, PO4.13 Ligand excluded by PLIP PO4.13: 4 residues within 4Å: Chain A: K.109, K.243 Ligands: PO4.12, PO4.14 Ligand excluded by PLIP PO4.14: 3 residues within 4Å: Chain A: R.188, K.243 Ligands: PO4.13 Ligand excluded by PLIP PO4.16: 4 residues within 4Å: Chain B: R.188, K.243 Ligands: PO4.17, PO4.18 Ligand excluded by PLIP PO4.17: 4 residues within 4Å: Chain B: K.109 Ligands: PO4.16, PO4.18, PO4.19 Ligand excluded by PLIP PO4.18: 7 residues within 4Å: Chain B: K.109, R.176, K.243 Ligands: PO4.16, PO4.17, PO4.19, PO4.20 Ligand excluded by PLIP PO4.19: 7 residues within 4Å: Chain B: K.96, K.109, E.241, K.243 Ligands: PO4.17, PO4.18, PO4.20 Ligand excluded by PLIP PO4.20: 10 residues within 4Å: Chain B: R.79, R.81, K.96, K.109, R.176 Ligands: PO4.18, PO4.19, PO4.21, PO4.22, PO4.23 Ligand excluded by PLIP PO4.21: 8 residues within 4Å: Chain B: Y.56, R.79, R.81, Y.174, R.176, K.273 Ligands: PO4.20, PO4.22 Ligand excluded by PLIP PO4.22: 7 residues within 4Å: Chain B: K.15, F.271, K.273 Ligands: PO4.20, PO4.21, PO4.23, PO4.24 Ligand excluded by PLIP PO4.23: 9 residues within 4Å: Chain B: Y.56, R.79, K.96, S.272, K.273, F.274 Ligands: PO4.20, PO4.22, PO4.24 Ligand excluded by PLIP PO4.24: 8 residues within 4Å: Chain B: K.15, R.68, K.96, F.271, S.272 Ligands: PO4.22, PO4.23, PO4.25 Ligand excluded by PLIP PO4.25: 7 residues within 4Å: Chain B: K.15, R.68, K.71, K.96, K.270 Ligands: PO4.24, PO4.26 Ligand excluded by PLIP PO4.26: 6 residues within 4Å: Chain B: K.71, H.98, S.107, K.270 Ligands: PO4.25, PO4.27 Ligand excluded by PLIP PO4.27: 5 residues within 4Å: Chain B: H.98, S.107, K.270 Ligands: PO4.26, PO4.28 Ligand excluded by PLIP PO4.28: 4 residues within 4Å: Chain B: K.106 Ligands: PO4.1, PO4.27, PO4.29 Ligand excluded by PLIP PO4.29: 4 residues within 4Å: Chain B: K.270 Ligands: PO4.1, PO4.28, PO4.30 Ligand excluded by PLIP PO4.30: 4 residues within 4Å: Ligands: PO4.1, PO4.2, PO4.3, PO4.29 Ligand excluded by PLIP

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

SO4.15: 4 residues within 4Å: Chain A: S.87, T.88, D.89, T.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.88, A:D.89, A:T.90 Water bridges: A:T.90 SO4.31: 3 residues within 4Å: Chain B: T.88, D.89, T.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.89, B:T.90, B:T.90 SO4.32: 2 residues within 4Å: Chain B: Y.159, K.163 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hothorn, M. et al., Catalytic core of a membrane-associated eukaryotic polyphosphate polymerase. Science (2009)

Release Date

2009-05-05

Peptides

Vacuolar transporter chaperone 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Vacuolar transporter chaperone 4

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