MolNFT v1 · #115888 · protein
Structure of XOO1075, a peptide deformylase from xanthomonas oryze pv oryzae, in complex with fragment 83
5CWY: “Structure of XOO1075, a peptide deformylase from xanthomonas oryze pv oryzae, in complex with fragment 83”. X-ray diffraction, 3 ligands (4WL, CD, NA), 2 pockets (best druggability 0.58). MolNFT v1 #115888 on GenesisL1: 3D…
- PDB
- 5CWY
- Type
- protein
- Length
- 168 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q5H3Z2
- Ligands
- 4WL, CD, NA
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 168 | 26% helix, 31% strand | Q5H3Z2 |
Ligands and binding sites
- 4WL · 4H-thieno[3,2-b]pyrole-5-carboxylic acid · ligand · chains A
- CD · Cadmium ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.58 | 0.85 | 23 | 4WL |
| 2 | 54 | 0.26 | 0.73 | 14 | empty |
Compared structures
- 5CWY · Structure of Xoo1075, a peptide deformylase from Xanthomonas oryze pv oryzae, in complex… · 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 Q5H3Z2
- Elsewhere: RCSB PDB 5CWY · PDBe 5CWY · UniProt Q5H3Z2
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