Research workbench
D-cysteine desulfhydrase from salmonella typhimurium complexed with D- cycloserine (dcs)
Analyse D-cysteine desulfhydrase from salmonella typhimurium complexed with D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D9F
- Type
- protein
- Length
- 1,293 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-cysteine desulfhydrase
- EC
- 4.4.1.15
- UniProt
- Q8ZNT7
- Ligands
- DCS, BEN
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 328 | 44% helix, 15% strand | Q8ZNT7 |
| B | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 320 | 45% helix, 15% strand | Q8ZNT7 |
| C | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 317 | 44% helix, 15% strand | Q8ZNT7 |
Ligands and binding sites
- DCS · D-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-N,O-cycloserylamide · ligand · 4 copies · chains A, B, C, D
- BEN · Benzamidine · ligand · 3 copies · chains A, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.80 | 0.86 | 50 | empty |
| 2 | 356 | 0.78 | 0.88 | 58 | empty |
| 3 | 118 | 0.77 | 0.96 | 34 | empty |
| 4 | 108 | 0.76 | 0.97 | 34 | empty |
| 5 | 301 | 0.68 | 0.83 | 41 | DCS |
Interfaces
5 interfaces between chains.
- C–D · 1570 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1561 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 449 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 401 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4D9F · D-Cysteine desulfhydrase from Salmonella typhimurium complexed with D-cycloserine (DCS) · the same entry in another collection · chain D against D, TM-score 1.00
- Q8ZNT7 · AlphaFold monomer V2.0 prediction for D-cysteine desulfhydrase (Q8ZNT7) · a predicted model of the same protein · chain D 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 Q8ZNT7
- Elsewhere: RCSB PDB 4D9F · PDBe 4D9F · UniProt Q8ZNT7
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