- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x TPW: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 4 residues within 4Å:- Chain A: D.452, N.479, G.481
- Ligands: TPW.1
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.452, A:G.481, H2O.10
MG.6: 4 residues within 4Å:- Chain B: D.452, N.479, G.481
- Ligands: TPW.5
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.452, B:G.481, H2O.22
MG.10: 4 residues within 4Å:- Chain C: D.452, N.479, G.481
- Ligands: TPW.9
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.452, C:G.481, H2O.34
MG.14: 4 residues within 4Å:- Chain D: D.452, N.479, G.481
- Ligands: TPW.13
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.452, D:G.481, H2O.46
- 4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.3: 20 residues within 4Å:- Chain A: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, Q.308, G.324, D.325, I.326, T.424
14 PLIP interactions:14 interactions with chain A- Hydrogen bonds: A:R.160, A:R.160, A:K.222, A:R.282, A:R.282, A:N.284, A:I.307, A:I.326, A:T.424, A:T.424
- Water bridges: A:D.325
- Salt bridges: A:K.222, A:K.222, A:R.282
ADP.7: 21 residues within 4Å:- Chain B: N.97, C.98, R.160, G.221, K.222, G.223, Y.226, A.227, M.247, G.280, A.281, R.282, N.284, L.286, M.287, D.306, I.307, G.324, D.325, I.326, T.424
13 PLIP interactions:13 interactions with chain B- Hydrogen bonds: B:R.160, B:R.160, B:K.222, B:R.282, B:R.282, B:N.284, B:I.307, B:I.326, B:T.424, B:T.424
- Salt bridges: B:K.222, B:K.222, B:R.282
ADP.11: 20 residues within 4Å:- Chain C: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, Q.308, G.324, D.325, I.326, T.424
14 PLIP interactions:14 interactions with chain C- Hydrogen bonds: C:R.160, C:R.160, C:K.222, C:R.282, C:R.282, C:N.284, C:I.307, C:I.326, C:T.424
- Water bridges: C:D.325, C:T.424
- Salt bridges: C:K.222, C:K.222, C:R.282
ADP.15: 21 residues within 4Å:- Chain D: N.97, C.98, R.160, G.221, K.222, G.223, Y.226, A.227, M.247, G.280, A.281, R.282, N.284, L.286, M.287, D.306, I.307, G.324, D.325, I.326, T.424
12 PLIP interactions:12 interactions with chain D- Hydrogen bonds: D:R.160, D:R.160, D:K.222, D:R.282, D:R.282, D:N.284, D:I.307, D:I.326, D:T.424
- Salt bridges: D:K.222, D:K.222, D:R.282
- 4 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)
B3P.4: 7 residues within 4Å:- Chain A: D.489, G.493, V.494, I.495, R.499
- Chain B: N.469, K.537
7 PLIP interactions:5 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:G.493, A:R.499, A:R.499, B:K.537, B:K.537
- Water bridges: A:D.489, A:S.496
B3P.8: 5 residues within 4Å:- Chain A: N.469
- Chain B: D.489, G.493, V.494, R.499
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:G.493, B:R.499, A:N.469
- Water bridges: B:I.495
B3P.12: 7 residues within 4Å:- Chain C: D.489, G.493, V.494, I.495, R.499
- Chain D: N.469, K.537
7 PLIP interactions:5 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:G.493, C:R.499, C:R.499, D:K.537, D:K.537
- Water bridges: C:D.489, C:S.496
B3P.16: 5 residues within 4Å:- Chain C: N.469
- Chain D: D.489, G.493, V.494, R.499
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:G.493, D:R.499, C:N.469
- Water bridges: D:I.495
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Berthold, C.L. et al., Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases. Structure (2007)
- Release Date
- 2007-07-17
- Peptides
- OXALYL-COA DECARBOXYLASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x TPW: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 4 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Berthold, C.L. et al., Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases. Structure (2007)
- Release Date
- 2007-07-17
- Peptides
- OXALYL-COA DECARBOXYLASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B