MolNFT v1 · #119683 · protein
Bacillus cereus formamidase (bceamif) acetylated at the active site.
5G3P: “Bacillus cereus formamidase (bceamif) acetylated at the active site.”. X-ray diffraction, 2 ligands (NA, PO4), 13 pockets (best druggability 0.56). MolNFT v1 #119683 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5G3P
- Type
- protein
- Length
- 1,954 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidase
- UniProt
- E5LR94
- Ligands
- NA, PO4
- Pockets
- 13 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formamidase | protein | 327 | 30% helix, 24% strand | E5LR94 |
| B, D | Formamidase | protein | 326 | 30% helix, 24% strand | E5LR94 |
| C, E, F | Formamidase | protein | 325 | 30% helix, 24% strand | E5LR94 |
Ligands and binding sites
- NA · Sodium ion · metal · 15 copies · chains A, B, E, F, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, C, E, A, D, F
- PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains A, B, E, C, D, F
- PGE · Triethylene glycol · additive · 6 copies · chains B, C, E, D, A, F
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, E
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.56 | 0.81 | 40 | PEG, NA |
| 2 | 147 | 0.54 | 0.81 | 27 | PGE |
| 3 | 124 | 0.53 | 0.81 | 26 | PEG |
| 4 | 134 | 0.53 | 0.81 | 27 | empty |
| 5 | 169 | 0.53 | 0.79 | 31 | PGE |
Interfaces
12 interfaces between chains.
- A–B · 4367 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 4341 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 4257 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 964 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 959 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (acetylation).
Compared structures
- 5G3P · Bacillus cereus formamidase (BceAmiF) acetylated at the active site. · 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 E5LR94
- Elsewhere: RCSB PDB 5G3P · PDBe 5G3P · UniProt E5LR94
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