MolNFT v1 · #88893 · protein
Crystal structure of D-cysteine desulfhydrase from salmonella typhimurium at 3.3 a in monoclinic space group with 8 subunits in the asymmetric unit
4D8U: “Crystal structure of D-cysteine desulfhydrase from salmonella typhimurium at 3.3 a in monoclinic space group…”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.79). MolNFT v1 #88893 on GenesisL1: 3D structure…
- PDB
- 4D8U
- Type
- protein
- Length
- 2,608 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-cysteine desulfhydrase
- EC
- 4.4.1.15
- UniProt
- Q8ZNT7
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 330 | 43% helix, 16% strand | Q8ZNT7 |
| B, C | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 323 | 44% helix, 15% strand | Q8ZNT7 |
| D | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 329 | 44% helix, 16% strand | Q8ZNT7 |
| F | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 318 | 44% helix, 16% strand | Q8ZNT7 |
| G | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 324 | 44% helix, 16% strand | Q8ZNT7 |
| H | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 331 | 44% helix, 15% strand | Q8ZNT7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.79 | 0.97 | 32 | empty |
| 2 | 139 | 0.79 | 0.96 | 34 | empty |
| 3 | 144 | 0.79 | 0.96 | 34 | empty |
| 4 | 129 | 0.78 | 0.96 | 35 | empty |
| 5 | 874 | 0.75 | 0.79 | 95 | PO4 |
Interfaces
13 interfaces between chains.
- C–D · 1548 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1499 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1482 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1470 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 498 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (cofactor).
Compared structures
- 4D8U · Crystal structure of D-Cysteine desulfhydrase from Salmonella typhimurium at 3.3 A in… · the same entry in another collection · chain H against H, TM-score 1.00
- Q8ZNT7 · AlphaFold monomer V2.0 prediction for D-cysteine desulfhydrase (Q8ZNT7) · a predicted model of the same protein · chain G 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 4D8U · PDBe 4D8U · UniProt Q8ZNT7
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