UniProt P00558
Phosphoglycerate kinase 1 (P00558)
Phosphoglycerate kinase 1 (UniProt P00558), EC 2.7.2.3: 48 experimental structures and 1 predicted model on GenesisL1, 5 ligands bound, 8 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- P00558
- Protein
- Phosphoglycerate kinase 1
- EC
- 2.7.2.3
- Experimental structures
- 48
- Predicted models
- 1
- Ligands
- 5
- Pockets
- 8 · 3 records with a druggable one
Structures
49 records of P00558 in the MolNFT archive: 48 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 2WZB | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 2WZB | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 2WZC | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 2WZC | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 2WZD | The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in… | x-ray diffraction | A | — | — |
| 2WZD | The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in… | x-ray diffraction | A | — | — |
| 2X13 | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 2X13 | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 2X14 | The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in… | x-ray diffraction | A | — | — |
| 2X14 | The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in… | x-ray diffraction | A | — | — |
| 2X15 | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 2X15 | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 2XE6 | The complete reaction cycle of human phosphoglycerate kinase: The open binary complex with 3PG | x-ray diffraction | A | — | — |
| 2XE6 | The complete reaction cycle of human phosphoglycerate kinase: the open binary complex with 3PG | x-ray diffraction | A | — | — |
| 2XE7 | The complete reaction cycle of human phosphoglycerate kinase: The open ternary complex with 3PG and… | x-ray diffraction | A | — | — |
| 2XE7 | The complete reaction cycle of human phosphoglycerate kinase: the open ternary complex with 3PG and… | x-ray diffraction | A | — | — |
| 2XE8 | The complete reaction cycle of human phosphoglycerate kinase: The open ternary complex with 3PG and… | x-ray diffraction | A | — | — |
| 2XE8 | The complete reaction cycle of human phosphoglycerate kinase: the open ternary complex with 3PG and… | x-ray diffraction | A | — | — |
| 2Y3I | The structure of the fully closed conformation of human PGK in complex with L-ADP, 3PG and the TSA… | x-ray diffraction | A, D | — | — |
| 2Y3I | The structure of the fully closed conformation of human pgk in complex with L-ADP, 3PG and the tsa… | x-ray diffraction | A, D | — | — |
| 2YBE | The structure of the fully closed conformation of human PGK in complex with L-ADP, 3PG and the TSA… | x-ray diffraction | A | — | — |
| 2YBE | The structure of the fully closed conformation of human pgk in complex with L-ADP, 3PG and the tsa… | x-ray diffraction | A | — | — |
| 2ZGV | Crystal Structure of human phosphoglycerate kinase bound to D-ADP | x-ray diffraction | A | — | — |
| 2ZGV | Crystal structure of human phosphoglycerate kinase bound to D-ADP | x-ray diffraction | A | — | — |
| 3C39 | Crystal Structure of human phosphoglycerate kinase bound to 3-phosphoglycerate | x-ray diffraction | A, B | — | — |
| 3C39 | Crystal structure of human phosphoglycerate kinase bound to 3-phosphoglycerate | x-ray diffraction | A, B | — | — |
| 3C3A | Crystal Structure of human phosphoglycerate kinase bound to 3-phosphoglycerate and L-ADP | x-ray diffraction | A, B | — | — |
| 3C3A | Crystal structure of human phosphoglycerate kinase bound to 3-phosphoglycerate and L-ADP | x-ray diffraction | A, B | — | — |
| 3C3B | Crystal Structure of human phosphoglycerate kinase bound to D-CDP | x-ray diffraction | A, B | — | — |
| 3C3B | Crystal structure of human phosphoglycerate kinase bound to D-cdp | x-ray diffraction | A, B | — | — |
| 3C3C | Crystal Structure of human phosphoglycerate kinase bound to 3-phosphoglycerate and L-CDP | x-ray diffraction | A, B | — | — |
| 3C3C | Crystal structure of human phosphoglycerate kinase bound to 3-phosphoglycerate and L-cdp | x-ray diffraction | A, B | — | — |
| 3ZOZ | The structure of human phosphoglycerate kinase with bound bromide, a stimulating anion. | x-ray diffraction | A | — | — |
| 3ZOZ | The structure of human phosphoglycerate kinase with bound bromide, a stimulating anion. | x-ray diffraction | A | — | — |
| 4AXX | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 4AXX | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with… | x-ray diffraction | A | — | — |
| 4O33 | Crystal Structure of human PGK1 3PG and terazosin(TZN) ternary complex | x-ray diffraction | A | — | — |
| 4O33 | Crystal structure of human PGK1 3PG and TERAZOSIN(TZN) ternary complex | x-ray diffraction | A | — | — |
| 5M1R | X-ray structure of human G166D PGK-1 mutant | x-ray diffraction | A | ADP, MG | 3 (best 0.52) |
| 5M1R | X-ray structure of human G166D pgk-1 mutant | x-ray diffraction | A | ADP, MG | — |
| 5M3U | The X-ray structure of human V216F phosphoglycerate kinase 1 mutant | x-ray diffraction | A | ADP, 3PG, MG | — |
| 5M6Z | The X-ray structure of human M189I PGK-1 mutant in partially closed conformation | x-ray diffraction | A | 3PG, PO4, ADP, MG | — |
| 5M6Z | The X-ray structure of human M189I pgk-1 mutant in partially closed conformation | x-ray diffraction | A | 3PG, PO4, ADP, MG | — |
| 5MXM | The X-ray structure of human M190I phosphoglycerate kinase 1 mutant | x-ray diffraction | A | MG, 3PG, ADP | — |
| 5NP8 | PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]pro… | x-ray diffraction | A | 93T, 3PG | — |
| 5NP8 | PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl… | x-ray diffraction | A | 93T, 3PG | — |
| 5O7D | The X-ray structure of human R38M phosphoglycerate kinase 1 mutant | x-ray diffraction | A | ADP | 2 (best 0.55) |
| 5O7D | The X-ray structure of human R38M phosphoglycerate kinase 1 mutant | x-ray diffraction | A | ADP | — |
| P00558 | AlphaFold monomer V2.0 prediction for phosphoglycerate kinase 1 (P00558) | predicted | A | — | 3 (best 0.52) |
Ligands
Experiment against prediction
- 5M3U chain A against the predicted model P00558: TM-score 1.00, RMSD 0.36 Å
- 5M1R chain A against the predicted model P00558: TM-score 1.00, RMSD 0.42 Å
- 5M1R chain A against the predicted model P00558: TM-score 1.00, RMSD 0.42 Å
- 5M6Z chain A against the predicted model P00558: TM-score 1.00, RMSD 0.48 Å
- 5M6Z chain A against the predicted model P00558: TM-score 1.00, RMSD 0.48 Å
- 5O7D chain A against the predicted model P00558: TM-score 0.99, RMSD 0.80 Å
- 5O7D chain A against the predicted model P00558: TM-score 0.99, RMSD 0.80 Å
- 2ZGV chain A against the predicted model P00558: TM-score 0.99, RMSD 0.87 Å
- 2ZGV chain A against the predicted model P00558: TM-score 0.99, RMSD 0.87 Å
- 5NP8 chain A against the predicted model P00558: TM-score 0.98, RMSD 0.96 Å
Elsewhere
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