- 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.4
MN.16: 8 residues within 4Å:- Chain B: D.442, L.443, N.469, G.471, G.472, Q.473
- Ligands: TD6.15, MG.17
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.442, B:G.471, H2O.34
- 3 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 9 residues within 4Å:- Chain A: G.441, 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.4
MG.7: 2 residues within 4Å:- Chain A: K.70, D.311
6 PLIP interactions:1 interactions with chain A, 5 Ligand-Water interactions- Metal complexes: A:D.311, H2O.1, H2O.2, H2O.6, H2O.9, H2O.9
MG.17: 8 residues within 4Å:- Chain B: D.442, L.443, N.469, G.471, G.472, Q.473
- Ligands: TD6.15, MN.16
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.442, B:G.471, H2O.34
- 3 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 10 residues within 4Å:- Chain A: H.49, H.50, T.51, H.52, L.61, R.430, A.453, L.454, Q.457
- Chain B: R.487
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:Q.457, B:R.487
GOL.18: 10 residues within 4Å:- Chain A: R.487
- Chain B: H.49, H.50, T.51, H.52, L.61, R.430, A.453, L.454, Q.457
9 PLIP interactions:7 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:H.49, B:T.51, B:T.51, B:R.430, B:R.430, B:L.454
- Water bridges: B:Q.457, A:R.487, A:R.487
GOL.19: 6 residues within 4Å:- Chain B: I.361, R.364, H.374, R.375, C.377, D.378
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:R.364, B:R.364, B:D.378, B:D.378, B:D.378
- 11 x FMT: FORMIC ACID(Non-functional Binders)
FMT.5: 8 residues within 4Å:- Chain A: P.123, G.124, S.133, I.134, S.135, H.165, I.166, N.167
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:G.124, A:I.134, A:I.134, A:H.165, A:N.167
FMT.6: 4 residues within 4Å:- Chain A: E.172, P.173, L.174, Y.175
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.174, A:Y.175
FMT.8: 2 residues within 4Å:- Chain A: K.70, S.230
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.70
- Water bridges: A:S.230, A:S.230
FMT.9: 7 residues within 4Å:- Chain A: R.121, P.123, G.124, M.125
- Chain B: A.127, S.128, H.129
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.128, B:S.128, B:H.129
FMT.10: 7 residues within 4Å:- Chain A: S.288, L.289, L.295, P.318
- Chain B: G.115, A.116, N.117
4 PLIP interactions:1 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:N.117
- Water bridges: A:S.288, A:S.288, A:L.289
FMT.11: 5 residues within 4Å:- Chain A: R.24, H.25, I.48, S.69, A.431
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.25
FMT.13: 7 residues within 4Å:- Chain A: G.31, S.32, R.33, T.78, R.107, Q.118
- Ligands: TD6.15
9 PLIP interactions:9 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:S.32, A:R.33, A:Q.118
FMT.14: 7 residues within 4Å:- Chain B: G.31, S.32, R.33, T.78, R.107, Q.118
- Ligands: TD6.1
9 PLIP interactions:9 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:S.32, B:R.33, B:Q.118
FMT.20: 3 residues within 4Å:- Chain B: K.197, P.198, R.201
No protein-ligand interaction detected (PLIP)FMT.21: 6 residues within 4Å:- Chain B: A.241, Q.242, W.246, P.247, L.248, P.259
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:W.246
- Water bridges: B:Q.242, B:Q.242, B:G.245
FMT.24: 7 residues within 4Å:- Chain A: G.115, A.116, N.117
- Chain B: S.288, L.289, L.295, P.318
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:L.289, A:N.117
- Water bridges: B:S.288
- 3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.12: 9 residues within 4Å:- Chain A: G.245, W.246, P.247, L.248, P.259, L.260, P.344, C.346, P.350
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.245
- Water bridges: A:G.245
EDO.22: 5 residues within 4Å:- Chain B: L.183, Q.186, Q.187, W.193, Q.194
1 PLIP interactions:1 interactions with chain B- Water bridges: B:Q.187
EDO.23: 4 residues within 4Å:- Chain A: R.487
- Chain B: F.47, I.48, H.49
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:R.487, B:H.49, B:H.49
- 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
EB
F
- 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)
- 3 x MG: MAGNESIUM ION(Non-covalent)
- 3 x GOL: GLYCEROL(Non-functional Binders)
- 11 x FMT: FORMIC ACID(Non-functional Binders)
- 3 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
EB
F