Research workbench
Crystal structure of a peptide deformylase from burkholderia xenovorans in complex with actinonin
Analyse Crystal structure of a peptide deformylase from burkholderia xenovorans in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VCP
- Type
- protein
- Length
- 640 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
- BB2, FE2, MG
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 159 | 30% helix, 31% strand | Q13XB1 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 161 | 29% helix, 34% strand | Q13XB1 |
| C | Peptide deformylase (EC 3.5.1.88) | protein | 161 | 30% helix, 37% strand | Q13XB1 |
| D | Peptide deformylase (EC 3.5.1.88) | protein | 159 | 31% helix, 35% strand | Q13XB1 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 4 copies · chains A, B, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.70 | 0.79 | 73 | MG |
| 2 | 134 | 0.48 | 0.79 | 19 | FE2, BB2 |
| 3 | 185 | 0.48 | 0.75 | 28 | empty |
| 4 | 124 | 0.47 | 0.79 | 21 | BB2 |
| 5 | 120 | 0.46 | 0.79 | 19 | BB2 |
Interfaces
5 interfaces between chains.
- A–C · 769 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 764 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 450 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 55 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5VCP · Crystal structure of a peptide deformylase from Burkholderia xenovorans in complex with… · 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 5VCP · PDBe 5VCP · UniProt Q13XB1
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