MolNFT v1 · #35143 · protein
Helicobacter pylori formamidase amif contains a fine-tuned cysteine- glutamate-lysine catalytic triad
2E2L: “Helicobacter pylori formamidase amif contains a fine-tuned cysteine- glutamate-lysine catalytic triad”. X-ray diffraction, 1 ligand (ARF), 5 pockets (best druggability 0.86). MolNFT v1 #35143 on GenesisL1: 3D structure, binding…
- PDB
- 2E2L
- Type
- protein
- Length
- 1,901 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidase
- EC
- 3.5.1.49
- UniProt
- O25836
- Ligands
- ARF
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Formamidase (EC 3.5.1.49) | protein | 317 | 30% helix, 22% strand | O25836 |
| E | Formamidase (EC 3.5.1.49) | protein | 316 | 30% helix, 22% strand | O25836 |
Ligands and binding sites
- ARF · Formamide · ligand · 3 copies · chains A, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.86 | 0.87 | 127 | empty |
| 2 | 1013 | 0.86 | 0.87 | 121 | empty |
| 3 | 729 | 0.84 | 0.87 | 99 | empty |
| 4 | 108 | 0.58 | 0.85 | 24 | empty |
| 5 | 97 | 0.56 | 0.85 | 20 | empty |
Interfaces
12 interfaces between chains.
- E–F · 4411 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 4402 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 4384 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 531 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 516 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2E2L · Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine… · the same entry in another collection · chain F against F, TM-score 1.00
- O25836 · AlphaFold monomer V2.0 prediction for formamidase (O25836) · a predicted model of the same protein · chain D 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 O25836
- Elsewhere: RCSB PDB 2E2L · PDBe 2E2L · UniProt O25836
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