Research workbench
Pdf protein is crystallized as NI2+ containing form, cocrystallized with inhibitor polyethylene glycol (peg)
Analyse Pdf protein is crystallized as NI2+ containing form, cocrystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ICJ
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.31
- UniProt
- P0A6K3
- Ligands
- NI, SO4
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Peptide deformylase (EC 3.5.1.31) | protein | 168 | 36% helix, 24% strand | P0A6K3 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- 2PE · Nonaethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.56 | 0.75 | 46 | 2PE |
| 2 | 260 | 0.55 | 0.77 | 37 | NI, 2PE |
| 3 | 126 | 0.50 | 0.80 | 23 | NI, 2PE |
| 4 | 109 | 0.36 | 0.74 | 23 | empty |
| 5 | 53 | 0.29 | 0.75 | 13 | empty |
Interfaces
2 interfaces between chains.
- B–C · 610 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1ICJ · Pdf protein is crystallized as NI2+ containing form, cocrystallized with inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6K3 · AlphaFold monomer V2.0 prediction for peptide deformylase (P0A6K3) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A6K3
- Elsewhere: RCSB PDB 1ICJ · PDBe 1ICJ · UniProt P0A6K3
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