- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x TPP: THIAMINE 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: TPP.1
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.452, A:G.481, H2O.10
MG.7: 4 residues within 4Å:- Chain B: D.452, N.479, G.481
- Ligands: TPP.6
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.452, B:G.481, H2O.23
MG.12: 4 residues within 4Å:- Chain C: D.452, N.479, G.481
- Ligands: TPP.11
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.452, C:G.481, H2O.34
MG.17: 4 residues within 4Å:- Chain D: D.452, N.479, G.481
- Ligands: TPP.16
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: 21 residues within 4Å:- Chain A: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, A.227, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, G.324, D.325, I.326, T.424
- Ligands: PGE.5
15 PLIP interactions:15 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:K.222, A:R.282
- Salt bridges: A:K.222, A:K.222, A:R.282
ADP.8: 20 residues within 4Å:- Chain B: N.97, C.98, R.160, G.221, K.222, G.223, Y.226, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, G.324, D.325, I.326, T.424
- Ligands: PGE.10
15 PLIP interactions:15 interactions with chain B- Hydrogen bonds: B:R.160, B:R.160, B:K.222, B:R.282, B:N.284, B:I.307, B:I.326, B:T.424, B:T.424
- Water bridges: B:K.222, B:K.222, B:A.250
- Salt bridges: B:K.222, B:K.222, B:R.282
ADP.13: 21 residues within 4Å:- Chain C: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, A.227, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, G.324, D.325, I.326, T.424
- Ligands: PGE.15
15 PLIP interactions:15 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:K.222, C:R.282, C:T.424
- Salt bridges: C:K.222, C:K.222, C:R.282
ADP.18: 20 residues within 4Å:- Chain D: N.97, C.98, R.160, G.221, K.222, G.223, Y.226, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, G.324, D.325, I.326, T.424
- Ligands: PGE.20
15 PLIP interactions:15 interactions with chain D- Hydrogen bonds: D:R.160, D:R.160, D:K.222, D:R.282, D:N.284, D:I.307, D:I.326, D:T.424
- Water bridges: D:K.222, D:K.222, D:A.250, D:T.424
- Salt bridges: D:K.222, D:K.222, D:R.282
- 4 x FYN: S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-9,13,15-TRIHYDROXY-10,10-DIMETHYL-13,15-DIOXIDO-4,8-DIOXO-12,14,16-TRIOXA-3,7-DIAZA-13,15-DIPHOSPHAHEPTADEC-1-YL} THIOFORMATE(Non-covalent)
FYN.4: 23 residues within 4Å:- Chain A: A.263, A.264, T.265, R.266, A.267, W.285, L.286, N.358, K.359, L.362, G.400, L.404, D.405, R.408, M.409, G.426, Y.483, S.553, R.555, I.556
- Chain B: I.34, Y.120
- Ligands: TPP.1
22 PLIP interactions:21 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:W.285, A:L.286, A:I.556
- Hydrogen bonds: A:A.263, A:R.266, A:A.267, A:R.408, A:R.408
- Water bridges: A:R.266, A:R.266, A:F.268, A:D.405, A:M.409, A:D.412, A:D.412, A:D.412, B:Y.120
- Salt bridges: A:R.266, A:R.408, A:R.555, A:R.555, A:R.555
FYN.9: 24 residues within 4Å:- Chain A: Y.120
- Chain B: A.263, A.264, T.265, R.266, A.267, W.285, L.286, N.358, K.359, L.362, G.400, A.401, L.404, D.405, R.408, M.409, G.426, M.428, Y.483, S.553, R.555, I.556
- Ligands: TPP.6
16 PLIP interactions:16 interactions with chain B- Hydrophobic interactions: B:L.404, B:I.556
- Hydrogen bonds: B:A.264, B:R.266, B:A.267, B:R.408, B:R.408, B:M.409
- Water bridges: B:R.385, B:A.401, B:D.405
- Salt bridges: B:R.266, B:R.408, B:R.408, B:R.555, B:R.555
FYN.14: 23 residues within 4Å:- Chain C: A.263, A.264, T.265, R.266, A.267, W.285, L.286, N.358, K.359, L.362, G.400, L.404, D.405, R.408, M.409, G.426, Y.483, S.553, R.555, I.556
- Chain D: I.34, Y.120
- Ligands: TPP.11
22 PLIP interactions:22 interactions with chain C- Hydrophobic interactions: C:W.285, C:L.286, C:I.556
- Hydrogen bonds: C:A.263, C:R.266, C:A.267, C:R.408, C:R.408, C:Y.483
- Water bridges: C:R.266, C:R.266, C:F.268, C:D.405, C:M.409, C:D.412, C:D.412, C:D.412
- Salt bridges: C:R.266, C:R.408, C:R.555, C:R.555, C:R.555
FYN.19: 24 residues within 4Å:- Chain C: Y.120
- Chain D: A.263, A.264, T.265, R.266, A.267, W.285, L.286, N.358, K.359, L.362, G.400, A.401, L.404, D.405, R.408, M.409, G.426, M.428, Y.483, S.553, R.555, I.556
- Ligands: TPP.16
18 PLIP interactions:18 interactions with chain D- Hydrophobic interactions: D:L.404, D:I.556
- Hydrogen bonds: D:A.264, D:R.266, D:A.267, D:R.408, D:R.408, D:M.409, D:Y.483
- Water bridges: D:R.385, D:A.401, D:D.405, D:D.412
- Salt bridges: D:R.266, D:R.408, D:R.408, D:R.555, D:R.555
- 4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.5: 7 residues within 4Å:- Chain A: E.70, G.71, A.193, Y.226, A.227, Q.228
- Ligands: ADP.3
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:P.194
- Water bridges: A:Y.226, A:Y.226
PGE.10: 8 residues within 4Å:- Chain B: E.70, G.71, A.193, P.194, Y.226, A.227, D.325
- Ligands: ADP.8
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.325
- Water bridges: B:Y.226
PGE.15: 7 residues within 4Å:- Chain C: E.70, G.71, A.193, Y.226, A.227, Q.228
- Ligands: ADP.13
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:P.194
PGE.20: 8 residues within 4Å:- Chain D: E.70, G.71, A.193, P.194, Y.226, A.227, D.325
- Ligands: ADP.18
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:D.325
- 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 2.15 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 4 x FYN: S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-9,13,15-TRIHYDROXY-10,10-DIMETHYL-13,15-DIOXIDO-4,8-DIOXO-12,14,16-TRIOXA-3,7-DIAZA-13,15-DIPHOSPHAHEPTADEC-1-YL} THIOFORMATE(Non-covalent)
- 4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 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