- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.34 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x TD6: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid(Non-covalent)
- 2 x MN: MANGANESE (II) ION(Non-covalent)
MN.2: 8 residues within 4Å:- Chain A: D.442, L.443, N.469, G.471, G.472, Q.473
- Ligands: TD6.1, MG.3
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.442, A:G.471, H2O.5
MN.18: 9 residues within 4Å:- Chain B: G.441, D.442, L.443, N.469, G.471, G.472, Q.473
- Ligands: TD6.17, MG.19
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.442, B:G.471, H2O.30
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 8 residues within 4Å:- Chain A: D.442, L.443, N.469, G.471, G.472, Q.473
- Ligands: TD6.1, MN.2
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.442, A:G.471, H2O.5
MG.5: 1 residues within 4Å:- Chain A: D.311
5 PLIP interactions:1 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:D.311, H2O.5, H2O.12, H2O.16, H2O.21
MG.19: 8 residues within 4Å:- Chain B: D.442, L.443, N.469, G.471, G.472, Q.473
- Ligands: TD6.17, MN.18
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.442, B:G.471, H2O.30
MG.23: 2 residues within 4Å:- Chain B: D.311
- Ligands: GOL.22
5 PLIP interactions:1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:D.311, H2O.30, H2O.37, H2O.41, H2O.43
- 4 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 10 residues within 4Å:- Chain A: H.49, H.50, T.51, H.52, R.430, A.453, L.454, Q.457
- Chain B: R.487
- Ligands: FMT.8
8 PLIP interactions:7 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:H.49, A:T.51, A:T.51, A:R.430, A:R.430, A:Q.457
- Water bridges: A:R.456, B:R.487
GOL.20: 9 residues within 4Å:- Chain A: R.487
- Chain B: H.49, H.50, T.51, H.52, R.430, A.453, L.454, Q.457
8 PLIP interactions:7 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:H.49, B:T.51, B:T.51, B:R.430, B:R.430, B:Q.457
- Water bridges: B:Q.457, A:R.487
GOL.22: 10 residues within 4Å:- Chain B: T.96, G.97, R.228, M.229, G.286, S.287, D.310, D.311, I.312
- Ligands: MG.23
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:R.228, B:R.228, B:R.228, B:S.287, B:D.310
- Water bridges: B:D.310, B:D.311, B:D.311, B:D.311
GOL.26: 5 residues within 4Å:- Chain B: Q.429, G.433, S.459, A.460, P.528
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:G.433, B:S.459, B:S.459
- Water bridges: B:G.433
- 12 x FMT: FORMIC ACID(Non-functional Binders)
FMT.6: 5 residues within 4Å:- Chain A: G.22, R.24, H.25, S.69, Q.71
No protein-ligand interaction detected (PLIP)FMT.7: 4 residues within 4Å:- Chain A: E.172, P.173, L.174, Y.175
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:L.174, A:Y.175
- Water bridges: A:E.172
FMT.8: 5 residues within 4Å:- Chain A: R.430, Q.457, V.458, S.459
- Ligands: GOL.4
No protein-ligand interaction detected (PLIP)FMT.9: 3 residues within 4Å:- Chain A: L.183, Q.186, W.193
No protein-ligand interaction detected (PLIP)FMT.11: 3 residues within 4Å:- Chain A: I.361, R.364
- Ligands: EDO.10
No protein-ligand interaction detected (PLIP)FMT.12: 7 residues within 4Å:- Chain A: M.357, H.374, C.377, L.400, S.401, Q.402
- Ligands: EDO.10
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.401, A:Q.402, A:Q.402
FMT.14: 7 residues within 4Å:- Chain A: S.288, L.289, L.295, P.318
- Chain B: G.115, A.116, N.117
7 PLIP interactions:6 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:L.289, B:N.117
- Water bridges: A:S.288, A:S.288, A:L.289, A:R.413, A:R.413
FMT.15: 7 residues within 4Å:- Chain A: G.31, S.32, R.33, T.78, R.107, Q.118
- Ligands: TD6.17
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:S.32, A:R.33, A:T.78, A:R.107, A:R.107, A:Q.118
- Water bridges: A:R.33
FMT.16: 7 residues within 4Å:- Chain B: G.31, S.32, R.33, T.78, R.107, Q.118
- Ligands: TD6.1
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:S.32, B:R.33, B:T.78, B:R.107, B:R.107, B:Q.118
- Water bridges: B:R.33
FMT.21: 4 residues within 4Å:- Chain A: R.487
- Chain B: F.47, I.48, H.49
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:R.487, B:H.49, B:H.49
- Water bridges: A:R.487
FMT.25: 7 residues within 4Å:- Chain B: T.290, G.291, K.292, R.293, R.395, L.477, L.546
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:R.395, B:R.395
- Water bridges: B:D.264, B:K.292, B:R.293
FMT.28: 6 residues within 4Å:- Chain B: W.246, P.247, L.260, P.344, C.346, P.350
1 PLIP interactions:1 interactions with chain B- Water bridges: B:C.346
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.10: 7 residues within 4Å:- Chain A: I.361, R.364, H.374, R.375, D.378
- Ligands: FMT.11, FMT.12
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.364, A:R.364, A:D.378
EDO.13: 3 residues within 4Å:- Chain A: L.295, Q.296, A.299
No protein-ligand interaction detected (PLIP)EDO.24: 8 residues within 4Å:- Chain A: G.115, A.116, N.117
- Chain B: S.288, L.289, L.295, P.318, R.413
7 PLIP interactions:1 interactions with chain A, 6 interactions with chain B- Hydrogen bonds: A:N.117, B:S.288, B:S.288
- Water bridges: B:S.288, B:S.288, B:L.289, B:L.289
EDO.27: 5 residues within 4Å:- Chain B: I.361, R.364, H.374, R.375, D.378
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.364, B:R.364, B:D.378
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Song, H.G. et al., A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis. J.Am.Chem.Soc. (2016)
- Release Date
- 2016-06-01
- Peptides
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GB
H
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.34 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x TD6: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid(Non-covalent)
- 2 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x GOL: GLYCEROL(Non-functional Binders)
- 12 x FMT: FORMIC ACID(Non-functional Binders)
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Song, H.G. et al., A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis. J.Am.Chem.Soc. (2016)
- Release Date
- 2016-06-01
- Peptides
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GB
H