SMTL ID : 3s5o.1

Crystal Structure of Human 4-hydroxy-2-oxoglutarate Aldolase Bound to Pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: E.39, K.43 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: K.43, F.275, G.276, Y.277 Ligand excluded by PLIP EDO.3: 8 residues within 4Å: Chain A: G.264, I.265, P.266, L.286 Chain B: Y.121, G.123, R.124 Ligands: EDO.6 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: V.22, T.23, P.25, L.37, N.40, L.44, N.224, M.272 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: W.274, F.275, W.306 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: S.57, N.153, T.260, G.264, I.265 Chain B: Y.121 Ligands: EDO.3 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain B: E.39, K.43 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain B: K.43, F.275, G.276, Y.277 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: Y.121, G.123, R.124 Chain B: G.264, I.265, P.266, L.286 Ligands: EDO.13 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain B: V.22, T.23, P.25, L.37, N.40, L.44, N.224, M.272 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: W.274, F.275, W.306 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: Y.121 Chain B: S.57, N.153, T.260, G.264, I.265 Ligands: EDO.10 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain C: E.39, K.43 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain C: K.43, F.275, G.276, Y.277 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain C: G.264, I.265, P.266, L.286 Chain D: Y.121, G.123, R.124 Ligands: EDO.20 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain C: V.22, T.23, P.25, L.37, N.40, L.44, N.224, M.272 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain C: W.274, F.275, W.306 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain C: S.57, N.153, T.260, G.264, I.265 Chain D: Y.121 Ligands: EDO.17 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain D: E.39, K.43 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain D: K.43, F.275, G.276, Y.277 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain C: Y.121, G.123, R.124 Chain D: G.264, I.265, P.266, L.286 Ligands: EDO.27 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain D: V.22, T.23, P.25, L.37, N.40, L.44, N.224, M.272 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain D: W.274, F.275, W.306 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain C: Y.121 Chain D: S.57, N.153, T.260, G.264, I.265 Ligands: EDO.24 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)

K.7: 4 residues within 4Å: Chain A: S.167, H.169, I.172, D.196 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.167, A:H.169, A:I.172, A:D.196, H2O.13, H2O.42 K.14: 4 residues within 4Å: Chain B: S.167, H.169, I.172, D.196 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.167, B:H.169, B:I.172, B:D.196, H2O.224, H2O.253 K.21: 4 residues within 4Å: Chain C: S.167, H.169, I.172, D.196 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.167, C:H.169, C:I.172, C:D.196, H2O.435, H2O.464 K.28: 4 residues within 4Å: Chain D: S.167, H.169, I.172, D.196 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.167, D:H.169, D:I.172, D:D.196, H2O.646, H2O.675

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riedel, T.J. et al., Structural and Biochemical Studies of Human 4-hydroxy-2-oxoglutarate Aldolase: Implications for Hydroxyproline Metabolism in Primary Hyperoxaluria. Plos One (2011)

Release Date

2011-10-26

Peptides

4-hydroxy-2-oxoglutarate aldolase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

4-hydroxy-2-oxoglutarate aldolase, mitochondrial