MolNFT v1 · #139358 · protein
Crystal structure of indole-bound tdsc from paenibacillus sp. A11-2
5XDC · Thermophilic dibenzothiophene desulfurization enzyme C: “Crystal structure of indole-bound tdsc from paenibacillus sp. A11-2”. X-ray diffraction, 2 ligands (IND, SO4), 17 pockets (best druggability 0.88). MolNFT v1 #139358 on…
- PDB
- 5XDC
- Type
- protein
- Length
- 1,600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermophilic dibenzothiophene desulfurization enzyme C
- UniProt
- Q9LBX2
- Ligands
- IND, SO4
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 401 | 58% helix, 11% strand | Q9LBX2 |
| B | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 402 | 59% helix, 11% strand | Q9LBX2 |
| D | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 396 | 58% helix, 11% strand | Q9LBX2 |
Ligands and binding sites
- IND · Indole · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.88 | 0.91 | 125 | SO4, IND |
| 2 | 736 | 0.85 | 0.88 | 88 | IND |
| 3 | 249 | 0.80 | 0.93 | 50 | IND, SO4 |
| 4 | 605 | 0.70 | 0.79 | 76 | empty |
| 5 | 325 | 0.59 | 0.77 | 34 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2093 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2064 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1781 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1707 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 140 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XDC · Crystal structure of Indole-bound TdsC from Paenibacillus sp. A11-2 · 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 Q9LBX2
- Elsewhere: RCSB PDB 5XDC · PDBe 5XDC · UniProt Q9LBX2
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