UniProt Q8L940
Pyridoxal 5'-phosphate synthase subunit PDX1.3 (Q8L940)
Pyridoxal 5'-phosphate synthase subunit PDX1.3 (UniProt Q8L940), EC 4.3.3.6: 28 experimental structures and 1 predicted model on GenesisL1, 11 ligands bound, 105 pockets. Binding sites, druggability and experiment against…
- UniProt
- Q8L940
- Protein
- Pyridoxal 5'-phosphate synthase subunit PDX1.3
- EC
- 4.3.3.6
- Experimental structures
- 28
- Predicted models
- 1
- Ligands
- 11
- Pockets
- 105 · 10 records with a druggable one
Structures
29 records of Q8L940 in the MolNFT archive: 28 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 5K2Z | PDX1.3-adduct (Arabidopsis) | x-ray diffraction | A, B, C, D | CL, SO4, 6R3 | — |
| 5K2Z | PDX1.3-adduct (arabidopsis) | x-ray diffraction | A, B, C, D | CL, SO4, 6R3 | — |
| 5K3V | apo-PDX1.3 (Arabidopsis) | x-ray diffraction | A, B, C, D | SO4, CL | 9 (best 0.80) |
| 5K3V | Apo-PDX1.3 (arabidopsis) | x-ray diffraction | A, B, C, D | SO4, CL | — |
| 5LNR | Crystal structure of Arabidopsis thaliana Pdx1-PLP complex | x-ray diffraction | A, B, C, D | PLP | 10 (best 0.65) |
| 5LNR | Crystal structure of arabidopsis thaliana PDX1-plp complex | x-ray diffraction | A, B, C, D | PLP | — |
| 5LNS | Crystal structure of Arabidopsis thaliana Pdx1-R5P complex | x-ray diffraction | A, B, C, D | 5RP, PO4 | — |
| 5LNS | Crystal structure of arabidopsis thaliana PDX1-R5P complex | x-ray diffraction | A, B, C, D | 5RP, PO4 | — |
| 5LNU | Crystal structure of Arabidopsis thaliana Pdx1-I320 complex | x-ray diffraction | A, B, C, D | PO4, SO4, KIK | — |
| 5LNU | Crystal structure of arabidopsis thaliana PDX1-I320 complex | x-ray diffraction | A, B, C, D | PO4, SO4, KIK | — |
| 5LNV | Crystal structure of Arabidopsis thaliana Pdx1-I320 complex from multiple crystals | x-ray diffraction | A, B, C, D | PO4, SO4, KIK | 8 (best 0.68) |
| 5LNV | Crystal structure of arabidopsis thaliana PDX1-I320 complex from multiple crystals | x-ray diffraction | A, B, C, D | PO4, SO4, KIK | — |
| 5LNW | Crystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex | x-ray diffraction | A, B, C, D | K8P, RP5, HG3 | 13 (best 0.73) |
| 5LNW | Crystal structure of arabidopsis thaliana PDX1-I320-G3P complex | x-ray diffraction | A, B, C, D | K8P, RP5, HG3 | — |
| 6HX3 | PDX1.2/PDX1.3 complex | x-ray diffraction | B, D, F, H | SO4 | — |
| 6HX3 | PDX1.2/PDX1.3 complex | x-ray diffraction | B, D, F, H | SO4 | — |
| 6HXG | PDX1.2/PDX1.3 complex (intermediate) | x-ray diffraction | B, D, F, H | SO4 | — |
| 6HXG | PDX1.2/PDX1.3 complex (intermediate) | x-ray diffraction | B, D, F, H | SO4 | — |
| 6HYE | PDX1.2/PDX1.3 complex (PDX1.3:K97A) | x-ray diffraction | B, D, F, H | SO4 | — |
| 6HYE | PDX1.2/PDX1.3 complex (PDX1.3:K97A) | x-ray diffraction | B, D, F, H | SO4 | — |
| 7LB6 | PDX1.2/PDX1.3 co-expression complex | electron microscopy | M, N, O, P, Q, R, S, T, U, V, W, X | — | 20 (best 0.66) |
| 7LB6 | PDX1.2/PDX1.3 co-expression complex | electron microscopy | M, N, O, P, Q, R, S, T, U, V, W, X | — | — |
| 7NHE | Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex | x-ray diffraction | A, B, C, D | PO4, KPR | 12 (best 0.74) |
| 7NHE | Crystal structure of arabidopsis thaliana PDX1K166R-I333 complex | x-ray diffraction | A, B, C, D | PO4, KPR | — |
| 7NHF | Crystal structure of Arabidopsis thaliana Pdx1K166R | x-ray diffraction | A, B, C, D | PO4 | 9 (best 0.68) |
| 7NHF | Crystal structure of arabidopsis thaliana PDX1K166R | x-ray diffraction | A, B, C, D | PO4 | — |
| 8S2W | SSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batch conditions | x-ray diffraction | A, B, C, D | PO4 | 11 (best 0.74) |
| 8S2X | SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets | x-ray diffraction | A, B, C, D | PO4 | 11 (best 0.73) |
| Q8L940 | AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit PDX1.3 (Q8L940) | predicted | A | — | 2 (best 0.74) |
Ligands
- SO4 · Sulfate ion · in 14 records
- PO4 · Phosphate ion · in 12 records
- CL · Chloride ion · in 4 records
- KIK · (4~{S})-4-azanyl-5-oxidanyl-pent-1-en-3-one · in 4 records
- 5RP · Ribulose-5-phosphate · in 2 records
- 6R3 · 2-azanylpenta-1,4-dien-3-one · in 2 records
- HG3 · [(2~{R})-2,3,3-tris(oxidanyl)propyl] dihydrogen phosphate · in 2 records
- K8P · [(2~{R},3~{R})-2,3-bis(oxidanyl)-3-[[(2~{S})-3-oxidanylidenepent-4-en-2-yl]amino]propyl] dihydrogen phosphate · in 2 records
- KPR · [(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate · in 2 records
- PLP · Pyridoxal-5'-phosphate · in 2 records
- RP5 · 5-O-phosphono-beta-D-ribofuranose · in 2 records
Experiment against prediction
- 7NHE chain B against the predicted model Q8L940: TM-score 1.00, RMSD 0.31 Å
- 7NHE chain B against the predicted model Q8L940: TM-score 1.00, RMSD 0.31 Å
- 7NHE chain D against the predicted model Q8L940: TM-score 1.00, RMSD 0.33 Å
- 7NHE chain D against the predicted model Q8L940: TM-score 1.00, RMSD 0.33 Å
- 6HX3 chain D against the predicted model Q8L940: TM-score 1.00, RMSD 0.37 Å
- 6HX3 chain D against the predicted model Q8L940: TM-score 1.00, RMSD 0.37 Å
- 5LNW chain D against the predicted model Q8L940: TM-score 1.00, RMSD 0.39 Å
- 5LNW chain D against the predicted model Q8L940: TM-score 1.00, RMSD 0.39 Å
- 6HYE chain B against the predicted model Q8L940: TM-score 1.00, RMSD 0.39 Å
- 6HYE chain B against the predicted model Q8L940: TM-score 1.00, RMSD 0.39 Å
Elsewhere
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