Research workbench
Cystathionine beta-synthase of mycobacterium tuberculosis in the presence of S-adenosylmethionine.
Analyse Cystathionine beta-synthase of mycobacterium tuberculosis in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XOH
- 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
- 17 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 30% 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 | 30% 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
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.88 | 0.90 | 153 | PLP |
| 2 | 1167 | 0.85 | 0.86 | 116 | PLP |
| 3 | 760 | 0.77 | 0.82 | 65 | PLP |
| 4 | 1104 | 0.76 | 0.79 | 94 | empty |
| 5 | 1090 | 0.76 | 0.79 | 91 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2030 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 2010 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1913 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 1892 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7XOH · Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of… · the same entry in another collection · chain B against B, 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 7XOH · PDBe 7XOH · UniProt P9WP51
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