MolNFT v1 · #85721 · protein
Peptide deformylase (ni-form) with hydrosulfide
4AL2: “Peptide deformylase (ni-form) with hydrosulfide”. X-ray diffraction, 2 ligands (NI, H2S), 5 pockets (best druggability 0.73). MolNFT v1 #85721 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4AL2
- Type
- protein
- Length
- 491 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- P0A6K3
- Ligands
- NI, H2S
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peptide deformylase (EC 3.5.1.88) | protein | 162 | 35% helix, 27% strand | P0A6K3 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 167 | 35% helix, 25% strand | P0A6K3 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
- H2S · Hydrosulfuric acid · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.73 | 0.76 | 98 | NI, H2S |
| 2 | 115 | 0.49 | 0.80 | 24 | H2S |
| 3 | 93 | 0.46 | 0.80 | 16 | H2S |
| 4 | 128 | 0.38 | 0.74 | 23 | empty |
| 5 | 76 | 0.34 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 537 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 298 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 4AL2 · PDBe 4AL2 · UniProt P0A6K3
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