SMTL ID : 1xkv.1

Crystal Structure Of ATP-Dependent Phosphoenolpyruvate Carboxykinase From Thermus thermophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: R.130, N.131, F.133, G.267 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.130, A:N.131, A:F.133, H2O.12 CA.5: 5 residues within 4Å: Chain B: R.130, N.131, F.133, G.267, P.323 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:R.130, B:N.131, B:F.133, H2O.15, H2O.19

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

PO4.2: 5 residues within 4Å: Chain A: V.20, S.21, P.22, R.130, R.137 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.21 Water bridges: A:S.21, A:S.21, A:R.137 Salt bridges: A:R.130, A:R.137 PO4.3: 5 residues within 4Å: Chain A: S.258, E.259, K.413, K.416, H.417 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.416, A:K.416 Salt bridges: A:K.413, A:K.416, A:H.417 PO4.6: 5 residues within 4Å: Chain B: V.20, S.21, P.22, R.130, R.137 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.21 Water bridges: B:S.21, B:S.21 Salt bridges: B:R.130, B:R.137 PO4.7: 4 residues within 4Å: Chain B: E.259, K.413, K.416, H.417 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.413, B:K.416 Salt bridges: B:K.413, B:K.416, B:H.417 PO4.8: 7 residues within 4Å: Chain B: L.233, S.234, G.235, T.236, G.237, K.238, T.239 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:L.233, B:G.235, B:T.236, B:G.237, B:K.238, B:T.239, B:T.239 Water bridges: B:G.235, B:T.239, B:T.240 PO4.9: 4 residues within 4Å: Chain B: E.5, H.10, P.11, K.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.3, B:E.5 Salt bridges: B:H.10, B:K.12

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

ATP.4: 15 residues within 4Å: Chain A: L.233, S.234, G.235, T.236, G.237, K.238, T.239, T.240, L.241, K.272, T.426, R.438, F.439, L.441, T.444 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.235, A:T.236, A:G.237, A:K.238, A:T.239, A:T.239, A:T.239, A:T.240, A:T.240, A:D.253, A:D.253, A:R.438, A:T.444, A:T.444 Water bridges: A:T.240, A:K.272 Salt bridges: A:K.238, A:K.238, A:K.272 pi-Cation interactions: A:R.438

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain B: Y.93, Y.159, F.160, Q.161, R.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.159, B:Q.161, B:R.166, B:R.166 GOL.11: 7 residues within 4Å: Chain A: E.66, G.67, W.71 Chain B: T.50, G.51, T.315, N.317 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.50, B:T.50, B:T.315 Water bridges: B:R.52, B:R.52, B:T.315, B:E.316, A:I.69, A:W.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugahara, M. et al., Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-10-11

Peptides

ATP-dependent phosphoenolpyruvate carboxykinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent phosphoenolpyruvate carboxykinase

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