MolNFT v1 · #119682 · protein
Bacillus cereus formamidase (bceamif) inhibited with urea.
5G3O: “Bacillus cereus formamidase (bceamif) inhibited with urea.”. X-ray diffraction, 2 ligands (P4G, PO4), 12 pockets (best druggability 0.81). MolNFT v1 #119682 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5G3O
- Type
- protein
- Length
- 1,659 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidase
- EC
- 3.5.1.49
- UniProt
- E5LR94
- Ligands
- P4G, PO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formamidase (EC 3.5.1.49) | protein | 277 | 31% helix, 27% strand | E5LR94 |
| B | Formamidase (EC 3.5.1.49) | protein | 275 | 32% helix, 27% strand | E5LR94 |
| C | Formamidase (EC 3.5.1.49) | protein | 274 | 32% helix, 27% strand | E5LR94 |
| D | Formamidase (EC 3.5.1.49) | protein | 278 | 32% helix, 27% strand | E5LR94 |
| E | Formamidase (EC 3.5.1.49) | protein | 278 | 31% helix, 27% strand | E5LR94 |
| F | Formamidase (EC 3.5.1.49) | protein | 277 | 31% helix, 27% strand | E5LR94 |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 2 copies · chains C, F, B
- PO4 · Phosphate ion · ion · 2 copies · chains B, E, F, A, C, D
- PEG · Di(hydroxyethyl)ether · additive · 23 copies · chains A, C, F, B, D, E
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.81 | 0.82 | 140 | PEG, P4G |
| 2 | 949 | 0.81 | 0.82 | 110 | PEG |
| 3 | 557 | 0.78 | 0.85 | 67 | empty |
| 4 | 197 | 0.58 | 0.80 | 29 | empty |
| 5 | 128 | 0.56 | 0.83 | 24 | empty |
Interfaces
12 interfaces between chains.
- D–E · 2092 Ų buried · 32 hydrogen bonds · protein-protein
- A–F · 2079 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2067 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 623 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 618 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
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 E5LR94
- Elsewhere: RCSB PDB 5G3O · PDBe 5G3O · UniProt E5LR94
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