Research workbench
K1U bound crystal structure of class I type B peptide deformylase from pseudomonas aeruginosa
Analyse K1U bound crystal structure of class I type B peptide deformylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JFD
- Type
- protein
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- A0A1C7BES9
- Ligands
- K1U, NI
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Peptide deformylase (EC 3.5.1.88) | protein | 160 | 28% helix, 34% strand | A0A1C7BES9 |
| C | Peptide deformylase (EC 3.5.1.88) | protein | 159 | 27% helix, 34% strand | A0A1C7BES9 |
Ligands and binding sites
- K1U · (3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl) sulfanyl]butanoic acid · ligand · chains C
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.79 | 0.80 | 79 | empty |
| 2 | 563 | 0.62 | 0.74 | 44 | empty |
| 3 | 120 | 0.50 | 0.80 | 18 | NI |
| 4 | 135 | 0.49 | 0.79 | 22 | K1U |
| 5 | 109 | 0.47 | 0.80 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 459 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 264 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 178 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JFD · K1U bound crystal structure of class I type b peptide deformylase from Pseudomonas… · 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 A0A1C7BES9
- Elsewhere: RCSB PDB 6JFD · PDBe 6JFD · UniProt A0A1C7BES9
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