Research workbench
Native cystathionine beta-synthase of mycobacterium tuberculosis.
Analyse Native cystathionine beta-synthase of mycobacterium tuberculosis. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XNZ
- Type
- protein
- Length
- 1,832 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cystathionine beta-synthase RV1077
- EC
- 4.2.1.22
- UniProt
- P9WP51
- Ligands
- PLP
- Pockets
- 19 · best druggability 0.89
Structure
electron microscopy · 1 distinct chain · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Putative cystathionine beta-synthase RV1077 (EC 4.2.1.22) | protein | 458 | 35% helix, 16% strand | P9WP51 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.89 | 0.90 | 147 | PLP |
| 2 | 1114 | 0.89 | 0.90 | 149 | PLP |
| 3 | 897 | 0.75 | 0.79 | 85 | empty |
| 4 | 882 | 0.75 | 0.79 | 85 | empty |
| 5 | 408 | 0.61 | 0.76 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1983 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1981 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1888 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 1878 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7XNZ · Native cystathionine beta-synthase of Mycobacterium tuberculosis. · the same entry in another collection · chain A against A, TM-score 1.00
- P9WP51 · AlphaFold monomer V2.0 prediction for putative cystathionine beta- synthase RV1077… · a predicted model of the same protein · chain B against A, TM-score 0.74
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 P9WP51
- Elsewhere: RCSB PDB 7XNZ · PDBe 7XNZ · UniProt P9WP51
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