MolNFT v1 · #175963 · protein
The structure of thioesterase dcsb
7D78 · Dltd domain-containing protein: “The structure of thioesterase dcsb”. X-ray diffraction, 2 ligands (NA, CL), 7 pockets (best druggability 0.71). MolNFT v1 #175963 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7D78
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dltd domain-containing protein
- UniProt
- J4WAT9
- Ligands
- NA, CL
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Dltd domain-containing protein | protein | 297 | 35% helix, 20% strand | J4WAT9 |
| A | Dltd domain-containing protein | protein | 295 | 37% helix, 20% strand | J4WAT9 |
Ligands and binding sites
- NA · Sodium ion · metal · chains D
- CL · Chloride ion · ion · 2 copies · chains D
- GOL · Glycerol · additive · 3 copies · chains D, A
- EDO · 1,2-ethanediol · additive · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.71 | 0.80 | 45 | empty |
| 2 | 63 | 0.70 | 0.95 | 21 | GOL |
| 3 | 166 | 0.70 | 0.88 | 29 | GOL |
| 4 | 137 | 0.48 | 0.78 | 18 | empty |
| 5 | 85 | 0.45 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- D–A · 1801 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7D78 · The structure of thioesterase DcsB · the same entry in another collection · chain D against D, 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 J4WAT9
- Elsewhere: RCSB PDB 7D78 · PDBe 7D78 · UniProt J4WAT9
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