SMTL ID : 3s5n.1

Crystal Structure of Human 4-hydroxy-2-oxoglutarate Aldolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: S.164, H.166, I.169, D.193 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.164, A:H.166, A:I.169, A:D.193, H2O.2 K.9: 4 residues within 4Å: Chain B: S.164, H.166, I.169, D.193 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.164, B:H.166, B:I.169, B:D.193, H2O.3 K.17: 4 residues within 4Å: Chain C: S.164, H.166, I.169, D.193 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.164, C:H.166, C:I.169, C:D.193, H2O.5 K.25: 4 residues within 4Å: Chain D: S.164, H.166, I.169, D.193 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.164, D:H.166, D:I.169, D:D.193, H2O.7

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: T.189, R.190, Q.192, F.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.192, A:F.194 NA.10: 4 residues within 4Å: Chain B: T.189, R.190, Q.192, F.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.194, B:F.194 NA.18: 4 residues within 4Å: Chain C: T.189, R.190, Q.192, F.194 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.189, C:F.194 NA.26: 4 residues within 4Å: Chain D: T.189, R.190, Q.192, F.194 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.194, D:F.194

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

EDO.3: 5 residues within 4Å: Chain A: K.40, F.272, G.273, Y.274 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: K.40 Ligands: EDO.3 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: V.19, T.20, P.22, L.34, N.37, L.41, N.221, M.269 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: T.257, R.258, R.259, F.260, G.261 Chain B: G.120, R.121 Ligands: EDO.8 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: S.54, N.55, N.150, T.257, G.261, I.262 Chain B: Y.118 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 9 residues within 4Å: Chain A: G.261, I.262, P.263, L.283 Chain B: Y.118, G.120, R.121 Ligands: EDO.6, EDO.7 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: K.40, F.272, G.273, Y.274 Ligands: EDO.12 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain B: K.40 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain B: V.19, T.20, P.22, L.34, N.37, L.41, N.221, M.269 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: G.120, R.121 Chain B: T.257, R.258, R.259, F.260, G.261 Ligands: EDO.16 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: Y.118 Chain B: S.54, N.55, N.150, T.257, G.261, I.262 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: Y.118, G.120, R.121 Chain B: G.261, I.262, P.263, L.283 Ligands: EDO.14, EDO.15 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: K.40, F.272, G.273, Y.274 Ligands: EDO.20 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain C: K.40 Ligands: EDO.19 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain C: V.19, T.20, P.22, L.34, N.37, L.41, N.221, M.269 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain C: T.257, R.258, R.259, F.260, G.261 Chain D: G.120, R.121 Ligands: EDO.24 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain C: S.54, N.55, N.150, T.257, G.261, I.262 Chain D: Y.118 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 9 residues within 4Å: Chain C: G.261, I.262, P.263, L.283 Chain D: Y.118, G.120, R.121 Ligands: EDO.22, EDO.23 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain D: K.40, F.272, G.273, Y.274 Ligands: EDO.28 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain D: K.40 Ligands: EDO.27 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain D: V.19, T.20, P.22, L.34, N.37, L.41, N.221, M.269 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain C: G.120, R.121 Chain D: T.257, R.258, R.259, F.260, G.261 Ligands: EDO.32 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain C: Y.118 Chain D: S.54, N.55, N.150, T.257, G.261, I.262 Ligands: EDO.32 Ligand excluded by PLIP EDO.32: 9 residues within 4Å: Chain C: Y.118, G.120, R.121 Chain D: G.261, I.262, P.263, L.283 Ligands: EDO.30, EDO.31 Ligand excluded by PLIP

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