MolNFT v1 · #7290 · protein
The crystal structure of E.COLI peptide deformylase complexed with actinonin
1G2A · Polypeptide deformylase: “The crystal structure of E.COLI peptide deformylase complexed with actinonin”. X-ray diffraction, 2 ligands (BB2, NI), 4 pockets (best druggability 0.57). MolNFT v1 #7290 on GenesisL1: 3D structure, binding…
- PDB
- 1G2A
- Type
- protein
- Length
- 492 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide deformylase
- EC
- 3.5.1.31
- UniProt
- P0A6K3
- Ligands
- BB2, NI
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Polypeptide deformylase (EC 3.5.1.31) | protein | 164 | 35% helix, 29% strand | P0A6K3 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.57 | 0.76 | 35 | BB2 |
| 2 | 187 | 0.54 | 0.79 | 33 | BB2 |
| 3 | 157 | 0.52 | 0.79 | 24 | BB2 |
| 4 | 118 | 0.38 | 0.75 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 627 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 273 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1G2A · The crystal structure of E.COLI peptide deformylase complexed with actinonin · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6K3 · AlphaFold monomer V2.0 prediction for peptide deformylase (P0A6K3) · a predicted model of the same protein · chain B 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 P0A6K3
- Elsewhere: RCSB PDB 1G2A · PDBe 1G2A · UniProt P0A6K3
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