MolNFT v1 · #63535 · protein
Crystal structure of a nudix hydrolase from clostridium perfringens
3FCM · Hydrolase, nudix family: “Crystal structure of a nudix hydrolase from clostridium perfringens”. X-ray diffraction, 1 ligand (MN), 3 pockets (best druggability 0.62). MolNFT v1 #63535 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3FCM
- Type
- protein
- Length
- 363 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase, nudix family
- UniProt
- Q0TTC5
- Ligands
- MN
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase, nudix family | protein | 180 | 32% helix, 32% strand | Q0TTC5 |
| B | Hydrolase, nudix family | protein | 183 | 32% helix, 29% strand | Q0TTC5 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.62 | 0.77 | 28 | empty |
| 2 | 447 | 0.61 | 0.76 | 39 | empty |
| 3 | 348 | 0.60 | 0.77 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3FCM · Crystal structure of a NUDIX hydrolase from Clostridium perfringens · 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 Q0TTC5
- Elsewhere: RCSB PDB 3FCM · PDBe 3FCM · UniProt Q0TTC5
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