UniProt P0A6K3
Protein (peptide deformylase) (P0A6K3)
Protein (peptide deformylase) (UniProt P0A6K3), EC 3.5.1.27, 3.5.1.31: 59 experimental structures and 1 predicted model on GenesisL1, 10 ligands bound, 58 pockets. Binding sites, druggability and experiment against prediction…
- UniProt
- P0A6K3
- Protein
- Protein (peptide deformylase)
- EC
- 3.5.1.27, 3.5.1.31, 3.5.1.88
- Experimental structures
- 59
- Predicted models
- 1
- Ligands
- 10
- Pockets
- 58 · 11 records with a druggable one
Structures
60 records of P0A6K3 in the MolNFT archive: 59 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 1BS4 | Peptide deformylase as ZN2+ containing form (native) in complex with inhibitor polyethylene glycol | x-ray diffraction | A, B, C | ZN, SO4 | 6 (best 0.55) |
| 1BS4 | Peptide deformylase as ZN2+ containing form (native) in complex with inhibitor polyethylene glycol | x-ray diffraction | A, B, C | — | — |
| 1BS5 | Peptide deformylase as ZN2+ containing form | x-ray diffraction | A, B, C | ZN, SO4 | 5 (best 0.58) |
| 1BS5 | Peptide deformylase as ZN2+ containing form | x-ray diffraction | A, B, C | — | — |
| 1BS6 | Peptide deformylase as NI2+ containing form in complex with tripeptide met-ala-ser | x-ray diffraction | A, B, C | NI, SO4 | 3 (best 0.45) |
| 1BS6 | Peptide deformylase as NI2+ containing form in complex with tripeptide met-ala-ser | x-ray diffraction | A, B, C | — | — |
| 1BS7 | Peptide deformylase as NI2+ containing form | x-ray diffraction | A, B, C | NI, SO4 | 4 (best 0.62) |
| 1BS7 | Peptide deformylase as NI2+ containing form | x-ray diffraction | A, B, C | — | — |
| 1BS8 | Peptide deformylase as ZN2+ containing form in complex with tripeptide met-ala-ser | x-ray diffraction | A, B, C | ZN, SO4 | 3 (best 0.44) |
| 1BS8 | Peptide deformylase as ZN2+ containing form in complex with tripeptide met-ala-ser | x-ray diffraction | A, B, C | — | — |
| 1BSJ | Cobalt deformylase inhibitor complex from E.COLI | x-ray diffraction | A | CO, PO4, MLN | 1 (best 0.51) |
| 1BSJ | Cobalt deformylase inhibitor complex from E.COLI | x-ray diffraction | A | — | — |
| 1BSK | Zinc deformylase inhibitor complex from E.COLI | x-ray diffraction | A | ZN, PO4, MLN | 1 (best 0.51) |
| 1BSK | Zinc deformylase inhibitor complex from E.COLI | x-ray diffraction | A | — | — |
| 1BSZ | Peptide deformylase as FE2+ containing form (native) in complex with inhibitor polyethylene glycol | x-ray diffraction | A, B, C | FE, SO4 | 4 (best 0.57) |
| 1BSZ | Peptide deformylase as FE2+ containing form (native) in complex with inhibitor polyethylene glycol | x-ray diffraction | A, B, C | — | — |
| 1DEF | Peptide deformylase catalytic core (residues 1-147), NMR, 9 structures | solution nmr | A | ZN | 3 (best 0.45) |
| 1DEF | Peptide deformylase catalytic core (residues 1-147), NMR, 9 structures | solution nmr | A | — | — |
| 1DFF | Peptide deformylase | x-ray diffraction | A | ZN | 2 (best 0.44) |
| 1DFF | Peptide deformylase | x-ray diffraction | A | — | — |
| 1G27 | Crystal structure of E.COLI polypeptide deformylase complexed with the inhibitor bb-3497 | x-ray diffraction | A, B, C | NI, BB1 | 4 (best 0.54) |
| 1G27 | Crystal structure of E.COLI polypeptide deformylase complexed with the inhibitor bb-3497 | x-ray diffraction | A, B, C | — | — |
| 1G2A | The crystal structure of E.COLI peptide deformylase complexed with actinonin | x-ray diffraction | A, B, C | NI, BB2 | 4 (best 0.57) |
| 1G2A | The crystal structure of E.COLI peptide deformylase complexed with actinonin | x-ray diffraction | A, B, C | — | — |
| 1ICJ | Pdf protein is crystallized as NI2+ containing form, cocrystallized with inhibitor polyethylene… | x-ray diffraction | A, B, C | NI, SO4 | 5 (best 0.56) |
| 1ICJ | Pdf protein is crystallized as NI2+ containing form, cocrystallized with inhibitor polyethylene… | x-ray diffraction | A, B, C | — | — |
| 1LRU | Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin | x-ray diffraction | A, B, C | ZN, BB2, SO4 | 3 (best 0.56) |
| 1LRU | Crystal structure of E.COLI peptide deformylase complexed with antibiotic actinonin | x-ray diffraction | A, B, C | — | — |
| 1XEM | High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate | x-ray diffraction | A | ZN | 1 (best 0.47) |
| 1XEM | High resolution crystal structure of escherichia COLI zinc- peptide deformylase bound to formate | x-ray diffraction | A | — | — |
| 1XEN | High Resolution Crystal Structure of Escherichia coli Iron- Peptide Deformylase Bound To Formate | x-ray diffraction | A | FE | 1 (best 0.49) |
| 1XEN | High resolution crystal structure of escherichia COLI iron- peptide deformylase bound to formate | x-ray diffraction | A | — | — |
| 1XEO | High Resolution Crystals Structure of Cobalt- Peptide Deformylase Bound To Formate | x-ray diffraction | A | CO | 1 (best 0.48) |
| 1XEO | High resolution crystals structure of cobalt- peptide deformylase bound to formate | x-ray diffraction | A | — | — |
| 2AI8 | E.coli Polypeptide Deformylase complexed with SB-485343 | x-ray diffraction | A, B, C | NI, SB7 | 5 (best 0.66) |
| 2AI8 | E.COLI polypeptide deformylase complexed with sb-485343 | x-ray diffraction | A, B, C | — | — |
| 2DEF | Peptide deformylase catalytic core (residues 1-147), NMR, 20 structures | solution nmr | A | — | — |
| 2DEF | Peptide deformylase catalytic core (residues 1-147), NMR, 20 structures | solution nmr | A | — | — |
| 2KMN | Solution structure of peptide deformylase complexed with actinonin | solution nmr | A | — | — |
| 2KMN | Solution structure of peptide deformylase complexed with actinonin | solution nmr | A | — | — |
| 2W3T | Chloro complex of the Ni-Form of E.coli deformylase | x-ray diffraction | A | — | — |
| 2W3T | Chloro complex of the ni-form of E.COLI deformylase | x-ray diffraction | A | — | — |
| 2W3U | formate complex of the Ni-Form of E.coli deformylase | x-ray diffraction | A | — | — |
| 2W3U | Formate complex of the ni-form of E.COLI deformylase | x-ray diffraction | A | — | — |
| 3K6L | The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827 | x-ray diffraction | A, B, C | — | — |
| 3K6L | The structure of E.COLI peptide deformylase (pdf) in complex with peptidomimetic ligand BB2827 | x-ray diffraction | A, B, C | — | — |
| 4AL2 | peptide deformylase (Ni-form) with hydrosulfide | x-ray diffraction | A, B, C | — | — |
| 4AL2 | Peptide deformylase (ni-form) with hydrosulfide | x-ray diffraction | A, B, C | — | — |
| 4AL3 | peptide deformylase (Co-form) with mercaptoethanol | x-ray diffraction | A | — | — |
| 4AL3 | Peptide deformylase (co-form) with mercaptoethanol | x-ray diffraction | A | — | — |
| 4AZ4 | E.coli deformylase with Co(II) and hydrosulfide | x-ray diffraction | A | — | — |
| 4AZ4 | E.COLI deformylase with CO(II) and hydrosulfide | x-ray diffraction | A | — | — |
| 4V5B | Structure of PDF binding helix in complex with the ribosome. | x-ray diffraction | A5 | — | — |
| 6IY7 | E. coli peptide deformylase crystal structure fitted into the cryo-EM density map of E. coli 70S… | electron microscopy | P | — | — |
| 6IY7 | E. COLI peptide deformylase crystal structure fitted into the cryo-EM density MAP of E. COLI 70S… | electron microscopy | P | — | — |
| 6IZI | Crystal structure of E. coli peptide deformylase and methionine aminopeptidase fitted into the… | electron microscopy | P | — | 2 (best 0.44) |
| 6IZI | Crystal structure of E. COLI peptide deformylase and methionine aminopeptidase fitted into the… | electron microscopy | P | — | — |
| 7D6Z | Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and… | electron microscopy | g | — | — |
| 7D80 | Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase… | electron microscopy | 3 | — | — |
| P0A6K3 | AlphaFold monomer V2.0 prediction for peptide deformylase (P0A6K3) | predicted | A | — | — |
Ligands
- SO4 · Sulfate ion · in 8 records
- ZN · Zinc ion · in 8 records
- NI · Nickel (II) ion · in 6 records
- BB2 · Actinonin · in 2 records
- CO · Cobalt (II) ion · in 2 records
- FE · Fe (III) ion · in 2 records
- MLN · (S)-2-(phosphonoxy)caproyl-L-leucyl-P-nitroanilide · in 2 records
- PO4 · Phosphate ion · in 2 records
- BB1 · 2-[(formyl-hydroxy-amino)-methyl]-hexanoic acid (1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide · in 1 record
- SB7 · [hydroxy(3-phenylpropyl)amino]methanol · in 1 record
Experiment against prediction
- 1XEN chain A against the predicted model P0A6K3: TM-score 0.99, RMSD 0.37 Å
- 1XEN chain A against the predicted model P0A6K3: TM-score 0.99, RMSD 0.37 Å
- 1XEO chain A against the predicted model P0A6K3: TM-score 0.99, RMSD 0.38 Å
- 1XEO chain A against the predicted model P0A6K3: TM-score 0.99, RMSD 0.38 Å
- 1G27 chain B against the predicted model P0A6K3: TM-score 0.99, RMSD 0.41 Å
- 1G27 chain B against the predicted model P0A6K3: TM-score 0.99, RMSD 0.41 Å
- 1BSJ chain A against the predicted model P0A6K3: TM-score 0.99, RMSD 0.42 Å
- 1BSJ chain A against the predicted model P0A6K3: TM-score 0.99, RMSD 0.42 Å
- 1BSK chain A against the predicted model P0A6K3: TM-score 0.99, RMSD 0.42 Å
- 1BSK chain A against the predicted model P0A6K3: TM-score 0.99, RMSD 0.42 Å
Elsewhere
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