MolNFT v1 · #60312 · protein
Crystal structure of a putative dehydratase from the NTF2-like family (SAV_4671) from streptomyces avermitilis at 2.10 a resolution
3CNX · Uncharacterized protein: “Crystal structure of a putative dehydratase from the NTF2-like family (SAV_4671) from streptomyces…”. X-ray diffraction, 3 ligands (UNL, MG, CL), 5 pockets (best druggability 0.57). MolNFT v1 #60312 on…
- PDB
- 3CNX
- Type
- protein
- Length
- 432 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q82EE4
- Ligands
- UNL, MG, CL
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 138 | 33% helix, 40% strand | Q82EE4 |
| B | Uncharacterized protein | protein | 146 | 29% helix, 40% strand | Q82EE4 |
| C | Uncharacterized protein | protein | 148 | 29% helix, 40% strand | Q82EE4 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
- PGE · Triethylene glycol · additive · chains A
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.57 | 0.83 | 22 | UNL |
| 2 | 128 | 0.56 | 0.82 | 21 | UNL |
| 3 | 129 | 0.55 | 0.82 | 18 | UNL, GOL |
| 4 | 192 | 0.45 | 0.74 | 35 | empty |
| 5 | 118 | 0.39 | 0.74 | 28 | MG |
Interfaces
2 interfaces between chains.
- A–B · 1462 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 608 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3CNX · Crystal structure of a putative dehydratase from the NTF2-like family (SAV_4671) from… · 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 Q82EE4
- Elsewhere: RCSB PDB 3CNX · PDBe 3CNX · UniProt Q82EE4
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