MolNFT v1 · #61805 · protein
Crystal structure of mycobacterium tuberculosis cysm, the cysteine synthase B
3DWI: “Crystal structure of mycobacterium tuberculosis cysm, the cysteine synthase B”. X-ray diffraction, 2 ligands (PLP, SO4), 4 pockets (best druggability 0.70). MolNFT v1 #61805 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3DWI
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine synthase B
- EC
- 2.5.1.47
- UniProt
- P63873
- Ligands
- PLP, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine synthase B (EC 2.5.1.47) | protein | 297 | 42% helix, 20% strand | P63873 |
| B | Cysteine synthase B (EC 2.5.1.47) | protein | 309 | 41% helix, 19% strand | P63873 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.70 | 0.80 | 76 | SO4 |
| 2 | 54 | 0.69 | 0.97 | 24 | empty |
| 3 | 308 | 0.58 | 0.77 | 41 | PLP |
| 4 | 134 | 0.58 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2096 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3DWI · Crystal structure of Mycobacterium tuberculosis CysM, the cysteine synthase B · 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 P63873
- Elsewhere: RCSB PDB 3DWI · PDBe 3DWI · UniProt P63873
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