SMTL ID : 3fd5.1

Crystal structure of human selenophosphate synthetase 1 complex with AMPCP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

AP2.1: 25 residues within 4Å: Chain A: K.34, L.40, L.44, L.47, I.68, G.69, M.70, D.71, D.89, D.112, T.269, F.271, H.276 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, K.6 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.34, A:K.34, A:G.69, A:M.70, A:M.70, A:D.112, A:T.269, A:T.269, B:G.164, B:T.166, B:T.166 Water bridges: B:G.164, B:T.166 AP2.7: 25 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.89, D.112, T.269, F.271, H.276 Ligands: PO4.8, MG.9, MG.10, K.11, MG.12 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:G.164, A:T.166, B:K.34, B:K.34, B:G.69, B:M.70, B:D.71, B:D.112, B:T.269, B:T.269 Water bridges: A:G.164, B:D.71, B:T.72, B:T.88, B:H.276

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

PO4.2: 9 residues within 4Å: Chain A: K.34, D.89, T.269, G.270, H.276 Chain B: Q.165 Ligands: AP2.1, MG.4, MG.5 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.269, A:T.269, A:G.270, B:Q.165 Water bridges: A:Y.90, A:N.108, A:N.108, A:N.108 Salt bridges: A:K.34 PO4.8: 10 residues within 4Å: Chain A: Q.165 Chain B: K.34, D.89, N.108, T.269, G.270, H.276 Ligands: AP2.7, MG.10, MG.12 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.269, B:G.270, A:Q.165, A:Q.165 Water bridges: B:D.89, B:N.108, B:N.108, B:N.108, B:E.321, 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: AP2.1, 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.8 MG.4: 6 residues within 4Å: Chain A: D.89, D.112 Ligands: AP2.1, PO4.2, MG.3, MG.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.89, A:D.112, H2O.1, H2O.10 MG.5: 5 residues within 4Å: Chain A: D.89 Chain B: Q.165 Ligands: AP2.1, PO4.2, MG.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.89, H2O.7 MG.9: 6 residues within 4Å: Chain B: D.71, D.112, D.267, T.269 Ligands: AP2.7, 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.16 MG.10: 8 residues within 4Å: Chain B: D.89, D.112, T.269 Ligands: AP2.7, PO4.8, MG.9, K.11, MG.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.89, B:D.112, H2O.11, H2O.18 MG.12: 5 residues within 4Å: Chain A: Q.165 Chain B: D.89 Ligands: AP2.7, PO4.8, MG.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.89, H2O.7

2 x K: POTASSIUM ION(Non-covalent)

K.6: 6 residues within 4Å: Chain A: D.71, T.87, T.88, D.89, D.112 Ligands: AP2.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.71, H2O.7 K.11: 7 residues within 4Å: Chain B: D.71, T.87, T.88, D.89, D.112 Ligands: AP2.7, MG.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.87

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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