MolNFT v1 · #124748 · protein
Crystal structure of a peptide deformylase from burkholderia xenovorans
5KOB: “Crystal structure of a peptide deformylase from burkholderia xenovorans”. X-ray diffraction, 1 ligand (FE2), 11 pockets (best druggability 0.70). MolNFT v1 #124748 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KOB
- Type
- protein
- Length
- 659 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q13XB1
- Ligands
- FE2
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 171 | 27% helix, 32% strand | Q13XB1 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 161 | 30% helix, 34% strand | Q13XB1 |
| C | Peptide deformylase (EC 3.5.1.88) | protein | 170 | 28% helix, 34% strand | Q13XB1 |
| D | Peptide deformylase (EC 3.5.1.88) | protein | 157 | 31% helix, 31% strand | Q13XB1 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 24 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.70 | 0.89 | 26 | empty |
| 2 | 168 | 0.51 | 0.78 | 27 | FE2, FMT, EDO |
| 3 | 231 | 0.49 | 0.74 | 35 | empty |
| 4 | 184 | 0.47 | 0.75 | 22 | empty |
| 5 | 102 | 0.44 | 0.79 | 19 | FE2, FMT |
Interfaces
5 interfaces between chains.
- B–D · 786 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 763 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 475 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 266 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 48 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5KOB · Crystal structure of a peptide deformylase from Burkholderia xenovorans · the same entry in another collection · chain A against A, TM-score 1.00
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 Q13XB1
- Elsewhere: RCSB PDB 5KOB · PDBe 5KOB · UniProt Q13XB1
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