SMTL ID : 3i7v.2 (1 other biounit)

Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 9 residues within 4Å: Chain A: S.6, K.31, G.32, Y.67, Y.69, K.78, Y.115 Ligands: EDO.4, EDO.7 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.6, A:S.6, A:K.31 Water bridges: A:K.31, A:N.33, A:T.70, A:G.117 Salt bridges: A:K.31, A:K.31, A:K.31, A:K.78, A:K.78, A:K.78 pi-Stacking: A:Y.67, A:Y.67, A:Y.115, A:Y.115

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.41, Y.61, K.81, Y.83 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.41, A:Y.83 GOL.3: 7 residues within 4Å: Chain A: E.41, I.58, L.59, D.60, Y.61, Y.83 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.60, A:D.60, A:Y.61

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: T.22, S.24, V.26, Y.115 Ligands: ATP.1, EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.22, A:S.24, A:Y.115 EDO.5: 2 residues within 4Å: Chain A: Y.67, W.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.68 Water bridges: A:H.66 EDO.6: 3 residues within 4Å: Chain A: L.113, K.114, K.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.113, A:K.119 EDO.7: 8 residues within 4Å: Chain A: S.28, K.31, I.65, Y.82, Y.115, D.118 Ligands: ATP.1, EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.28, A:K.31, A:D.118 Water bridges: A:K.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeyakanthan, J. et al., Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5. Acta Crystallogr.,Sect.D (2010)

Release Date

2009-07-21

Peptides

AP4A hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

AP4A hydrolase

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