UniProt P08397
Porphobilinogen deaminase (P08397)
Porphobilinogen deaminase (UniProt P08397), EC 2.5.1.61: 18 experimental structures and 1 predicted model on GenesisL1, 5 ligands bound, 13 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- P08397
- Protein
- Porphobilinogen deaminase
- EC
- 2.5.1.61
- Experimental structures
- 18
- Predicted models
- 1
- Ligands
- 5
- Pockets
- 13 · 3 records with a druggable one
Structures
19 records of P08397 in the MolNFT archive: 18 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3ECR | Structure of human porphobilinogen deaminase | x-ray diffraction | A, B | — | — |
| 3ECR | Structure of human porphobilinogen deaminase | x-ray diffraction | A, B | — | — |
| 3EQ1 | The Crystal Structure of Human Porphobilinogen Deaminase at 2.8A resolution | x-ray diffraction | A, B | — | — |
| 3EQ1 | The crystal structure of human porphobilinogen deaminase at 2.8A resolution | x-ray diffraction | A, B | — | — |
| 5M6R | Human porphobilinogen deaminase in complex with reaction intermediate | x-ray diffraction | A, B | 7J8, PO4 | 7 (best 0.77) |
| 5M6R | Human porphobilinogen deaminase in complex with reaction intermediate | x-ray diffraction | A, B | 7J8, PO4 | — |
| 5M7F | Human porphobilinogen deaminase in complex with DPM cofactor | x-ray diffraction | A, B | DPM, SO4 | — |
| 5M7F | Human porphobilinogen deaminase in complex with dpm cofactor | x-ray diffraction | A, B | DPM, SO4 | — |
| 7AAJ | Human porphobilinogen deaminase in complex with cofactor | x-ray diffraction | B, A | DPM | — |
| 7AAK | Human porphobilinogen deaminase R173W mutant crystallized in the ES2 intermediate state | x-ray diffraction | A, B | 7J8 | — |
| 7AAK | Human porphobilinogen deaminase R173W mutant crystallized in the ES2 intermediate state | x-ray diffraction | A, B | 7J8 | — |
| 7CCX | Crystal structure of the holo form of human hydroxymethylbilane synthase | x-ray diffraction | A, C | DPM | 3 (best 0.76) |
| 7CCX | Crystal structure of the holo form of human hydroxymethylbilane synthase | x-ray diffraction | A, C | DPM | — |
| 7CCY | Crystal structure of the 2-iodoporphobilinogen-bound holo form of human hydroxymethylbilane synthase | x-ray diffraction | A, C | DPM, FWL | — |
| 7CCZ | Crystal structure of the ES2 intermediate form of human hydroxymethylbilane synthase | x-ray diffraction | A, B | 7J8 | 3 (best 0.75) |
| 7CCZ | Crystal structure of the ES2 intermediate form of human hydroxymethylbilane synthase | x-ray diffraction | A, B | 7J8 | — |
| 7CD0 | Crystal structure of the 2-iodoporphobilinogen-bound ES2 intermediate form of human… | x-ray diffraction | A, B | 7J8, FWL | — |
| 7CD0 | Crystal structure of the 2-iodoporphobilinogen-bound ES2 intermediate form of human… | x-ray diffraction | A, B | 7J8, FWL | — |
| P08397 | AlphaFold monomer V2.0 prediction for porphobilinogen deaminase (P08397) | predicted | A | — | — |
Ligands
- 7J8 · 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid · in 8 records
- DPM · 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid · in 6 records
- FWL · 3-[5-(aminomethyl)-4-(carboxymethyl)-2-iodo-1H-pyrrol-3-yl]propanoic acid · in 3 records
- PO4 · Phosphate ion · in 2 records
- SO4 · Sulfate ion · in 2 records
Experiment against prediction
- 7CCY chain C against the predicted model P08397: TM-score 0.99, RMSD 0.57 Å
- 7CCX chain C against the predicted model P08397: TM-score 0.98, RMSD 0.84 Å
- 7CCX chain C against the predicted model P08397: TM-score 0.98, RMSD 0.84 Å
- 3EQ1 chain A against the predicted model P08397: TM-score 0.98, RMSD 1.07 Å
- 3EQ1 chain A against the predicted model P08397: TM-score 0.98, RMSD 1.07 Å
- 3ECR chain B against the predicted model P08397: TM-score 0.98, RMSD 1.29 Å
- 3ECR chain B against the predicted model P08397: TM-score 0.98, RMSD 1.29 Å
- 7CD0 chain B against the predicted model P08397: TM-score 0.97, RMSD 1.32 Å
- 7CD0 chain B against the predicted model P08397: TM-score 0.97, RMSD 1.32 Å
- 5M7F chain B against the predicted model P08397: TM-score 0.97, RMSD 1.34 Å
Elsewhere
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