SMTL ID : 3fd6.1

Crystal structure of human selenophosphate synthetase 1 complex with ADP and phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 23 residues within 4Å: Chain A: K.34, L.40, L.44, L.47, I.68, G.69, M.70, D.71, D.112, T.269, F.271 Chain B: M.126, L.128, V.161, G.163, G.164, Q.165, T.166 Ligands: PO4.2, MG.3, MG.4, MG.5, NA.6 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.69, A:M.70, A:D.112, A:T.269, A:T.269, B:T.166, B:T.166 Water bridges: A:M.70, B:G.164, B:G.164, B:T.166 Salt bridges: A:K.34, A:K.34 ADP.7: 22 residues within 4Å: Chain A: M.126, L.128, V.161, G.163, G.164, Q.165, T.166 Chain B: K.34, L.40, L.44, L.47, I.68, G.69, M.70, D.71, D.112, F.271 Ligands: PO4.8, MG.9, MG.10, MG.11, NA.12 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:G.164, A:T.166, B:G.69, B:G.69, B:D.71, B:D.112 Water bridges: A:G.164, A:G.164, A:T.166, B:D.71 Salt bridges: B:K.34, B:K.34

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

PO4.2: 9 residues within 4Å: Chain A: K.34, D.89, N.108, T.269, G.270 Chain B: Q.165 Ligands: ADP.1, MG.4, MG.5 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.89, A:D.89, A:N.108, A:T.269, A:T.269, A:G.270, B:Q.165 Salt bridges: A:K.34 PO4.8: 9 residues within 4Å: Chain A: Q.165 Chain B: K.34, D.89, N.108, T.269, G.270 Ligands: ADP.7, MG.10, MG.11 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.89, B:N.108, B:T.269, B:G.270, A:Q.165 Salt bridges: B:K.34

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.71, D.112, D.267 Ligands: ADP.1, MG.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.71, A:D.112, A:D.267, H2O.1, H2O.2 MG.4: 5 residues within 4Å: Chain A: D.112 Ligands: ADP.1, PO4.2, MG.3, MG.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.112, H2O.1, H2O.2, H2O.2 MG.5: 4 residues within 4Å: Chain B: Q.165 Ligands: ADP.1, PO4.2, MG.4 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain B: D.71, D.112, D.267 Ligands: ADP.7, MG.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.71, B:D.112, B:D.267, H2O.11, H2O.12 MG.10: 6 residues within 4Å: Chain B: D.89, D.112 Ligands: ADP.7, PO4.8, MG.9, MG.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.112, H2O.11, H2O.12, H2O.12 MG.11: 5 residues within 4Å: Chain A: Q.165 Chain B: D.89 Ligands: ADP.7, PO4.8, MG.10 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 5 residues within 4Å: Chain A: M.70, D.71, T.87, D.112 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.112 NA.12: 5 residues within 4Å: Chain B: D.71, T.87, T.88, D.112 Ligands: ADP.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.87, B:T.88 Water bridges: B:T.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, K.T. et al., Crystal structures of catalytic intermediates of human selenophosphate synthetase 1. J.Mol.Biol. (2009)

Release Date

2009-09-22

Peptides

Selenide, water dikinase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Selenide, water dikinase 1

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