MolNFT v1 · #71190 · protein
Crystal structure of arabidopsis thaliana peptide deformylase 1B (ATPDF1B) in complex with actinonin
3M6P: “Crystal structure of arabidopsis thaliana peptide deformylase 1B (ATPDF1B) in complex with actinonin”. X-ray diffraction, 2 ligands (BB2, ZN), 3 pockets (best druggability 0.53). MolNFT v1 #71190 on GenesisL1: 3D structure, binding…
- PDB
- 3M6P
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase 1B
- EC
- 3.5.1.88
- UniProt
- Q9FUZ2
- Ligands
- BB2, ZN
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase 1B (EC 3.5.1.88) | protein | 180 | 35% helix, 28% strand | Q9FUZ2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.53 | 0.81 | 24 | BB2 |
| 2 | 134 | 0.52 | 0.81 | 23 | BB2 |
| 3 | 89 | 0.33 | 0.73 | 20 | ZN |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3M6P · Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FUZ2 · AlphaFold monomer V2.0 prediction for peptide deformylase 1B, CHLOROPLASTIC/MITOCHONDRIAL… · 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 Q9FUZ2
- Elsewhere: RCSB PDB 3M6P · PDBe 3M6P · UniProt Q9FUZ2
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