Research workbench
Pyridoxamine 5' phosphate (pmp) bound form of salmonella typhimurium D-cysteine desulfhydrase obtained after co-crystallization with D- cycloserine
Analyse Pyridoxamine 5' phosphate (pmp) bound form of salmonella typhimurium D-cysteine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D9B
- Type
- protein
- Length
- 1,306 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
- PMP, BEN
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 328 | 47% helix, 15% strand | Q8ZNT7 |
| C | D-cysteine desulfhydrase (EC 4.4.1.15) | protein | 322 | 46% helix, 15% strand | Q8ZNT7 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- BEN · Benzamidine · ligand · 3 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.86 | 0.87 | 96 | EDO |
| 2 | 151 | 0.79 | 0.96 | 32 | empty |
| 3 | 139 | 0.78 | 0.96 | 35 | empty |
| 4 | 310 | 0.68 | 0.82 | 45 | PMP, EDO |
| 5 | 282 | 0.66 | 0.82 | 40 | PMP, EDO |
Interfaces
5 interfaces between chains.
- A–B · 1521 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1483 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 445 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 441 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 432 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4D9B · Pyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimurium D-Cysteine… · 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 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 Q8ZNT7
- Elsewhere: RCSB PDB 4D9B · PDBe 4D9B · UniProt Q8ZNT7
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