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Crystal structure of msm-13, a putative T1-like thiolase from mycobacterium smegmatis
Analyse Crystal structure of msm-13, a putative T1-like thiolase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BYV
- Type
- protein
- Length
- 4,768 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-ketothiolase
- UniProt
- A0QUH3
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Beta-ketothiolase | protein | 396 | 39% helix, 21% strand | A0QUH3 |
| B, C, G, L | Beta-ketothiolase | protein | 398 | 40% helix, 21% strand | A0QUH3 |
| E, J | Beta-ketothiolase | protein | 396 | 40% helix, 21% strand | A0QUH3 |
| F, K | Beta-ketothiolase | protein | 399 | 39% helix, 22% strand | A0QUH3 |
| H, M | Beta-ketothiolase | protein | 397 | 41% helix, 21% strand | A0QUH3 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.79 | 0.98 | 35 | empty |
| 2 | 107 | 0.78 | 0.98 | 33 | empty |
| 3 | 111 | 0.78 | 0.98 | 32 | empty |
| 4 | 107 | 0.78 | 0.97 | 35 | empty |
| 5 | 105 | 0.77 | 0.97 | 32 | empty |
Interfaces
25 interfaces between chains.
- E–F · 3042 Ų buried · 75 hydrogen bonds · protein-protein
- J–K · 3033 Ų buried · 78 hydrogen bonds · protein-protein
- A–B · 3020 Ų buried · 76 hydrogen bonds · protein-protein
- C–D · 2989 Ų buried · 75 hydrogen bonds · protein-protein
- G–H · 2988 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 5BYV · Crystal structure of MSM-13, a putative T1-like thiolase from Mycobacterium smegmatis · 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 A0QUH3
- Elsewhere: RCSB PDB 5BYV · PDBe 5BYV · UniProt A0QUH3
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