SMTL ID : 3i7u.1

Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

11 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: S.6, K.31, G.32, N.33, K.78 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: E.4, F.5, I.34 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: M.1, E.74, R.75 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: S.6, K.31, G.32, K.78 Ligands: PEG.11 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: K.31, Y.67, K.78 Chain C: L.71, K.72 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: S.6, K.31, G.32, K.78 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: L.71, K.72 Chain C: K.31, Y.67, K.78 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain D: S.6, G.32, K.78 Ligands: PEG.25 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain D: E.4, F.5, I.34 Ligands: EDO.7 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain D: K.55 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain D: M.1, E.74, R.75 Ligand excluded by PLIP

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

EDO.4: 4 residues within 4Å: Chain A: M.1, R.75 Chain C: H.66, W.68 No protein-ligand interaction detected (PLIP) EDO.7: 9 residues within 4Å: Chain B: I.34, E.35, P.36, G.37, E.38 Chain D: K.3, F.5, I.34 Ligands: CL.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.35, B:G.37, B:E.38 EDO.8: 6 residues within 4Å: Chain B: I.65, Y.67, Y.115, G.117, D.118 Chain C: K.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.117, B:D.118 EDO.9: 5 residues within 4Å: Chain A: K.39, P.40 Chain B: S.95, W.96, E.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.96, B:E.97 Water bridges: B:S.95 EDO.10: 4 residues within 4Å: Chain A: Y.61, I.62 Chain B: D.100, A.101 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.62 Water bridges: B:A.101 EDO.19: 4 residues within 4Å: Chain D: E.41, E.42, V.45, I.58 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain D: N.33, E.97 Ligands: PEG.25 4 PLIP interactions: 4 interactions with chain D Water bridges: D:N.33, D:R.46, D:E.47, D:E.47 EDO.21: 2 residues within 4Å: Chain D: R.75 Ligands: PG4.30 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.75 Water bridges: D:R.75 EDO.22: 3 residues within 4Å: Chain D: E.57, K.86, K.88 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.86, D:K.88 EDO.23: 5 residues within 4Å: Chain B: P.36 Chain C: W.96 Chain D: I.34, G.37, E.38 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:G.37, B:P.36 Water bridges: C:W.96 EDO.24: 4 residues within 4Å: Chain B: I.34 Chain C: E.97 Chain D: K.3, F.5 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Water bridges: C:E.97 Hydrogen bonds: D:K.3, B:I.34

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 4 residues within 4Å: Chain B: K.31, E.47, E.51 Ligands: CL.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.31 Water bridges: B:K.31, B:K.31, B:K.31, B:R.46 PEG.25: 8 residues within 4Å: Chain D: E.4, N.33, Y.69, L.71, K.78, E.97 Ligands: CL.15, EDO.20 3 PLIP interactions: 3 interactions with chain D Water bridges: D:E.4, D:E.4, D:N.33 PEG.26: 3 residues within 4Å: Chain D: T.70, G.73, R.75 No protein-ligand interaction detected (PLIP) PEG.27: 7 residues within 4Å: Chain C: K.99, D.100 Chain D: Y.61, G.63, E.64, I.121, K.124 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.100, D:E.64 Water bridges: C:K.21, C:K.21, D:K.124

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.14: 7 residues within 4Å: Chain C: P.92, D.100, A.101, K.102 Chain D: D.60, Y.61, I.62 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.100, D:I.62 Water bridges: C:R.93

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.28: 6 residues within 4Å: Chain D: Y.87, K.88, E.89, G.90, E.91, R.93 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.87, D:G.90, D:E.91, D:R.93, D:R.93 PGE.29: 8 residues within 4Å: Chain D: T.22, S.28, K.31, I.65, Y.115, K.116, G.117, D.118 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.28, D:K.31, D:K.116, D:G.117 Water bridges: D:T.22, D:Y.82

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.30: 5 residues within 4Å: Chain D: W.68, Y.69, T.70, R.75 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.70, D:T.70 Water bridges: D:R.75

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

AP4A hydrolase

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