Research workbench
Crystal structure of a peptide deformylase from haemophilus influenzae
Analyse Crystal structure of a peptide deformylase from haemophilus influenzae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WXK
- 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
- Q4QMV6
- Ligands
- NI
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase (EC 3.5.1.88) | protein | 164 | 35% helix, 26% strand | Q4QMV6 |
| C | Peptide deformylase (EC 3.5.1.88) | protein | 166 | 36% helix, 27% strand | Q4QMV6 |
| D | Peptide deformylase (EC 3.5.1.88) | protein | 165 | 36% helix, 27% strand | Q4QMV6 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.79 | 0.96 | 30 | GOL |
| 2 | 410 | 0.65 | 0.78 | 56 | GOL |
| 3 | 103 | 0.49 | 0.81 | 22 | empty |
| 4 | 97 | 0.47 | 0.81 | 17 | GOL |
| 5 | 170 | 0.44 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 882 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 585 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 493 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4WXK · Crystal structure of a peptide deformylase from Haemophilus influenzae · the same entry in another collection · chain D against D, TM-score 1.00
- Q4QMV6 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q4QMV6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q4QMV6
- Elsewhere: RCSB PDB 4WXK · PDBe 4WXK · UniProt Q4QMV6
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