Research workbench
Mycobacterium tuberculosis pknb kinase domain L33D mutant (crystal form 1)
Analyse Mycobacterium tuberculosis pknb kinase domain L33D mutant (crystal form 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ORI
- Type
- protein
- Length
- 1,068 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE protein kinase
- UniProt
- A5TY84
- Ligands
- AGS, MN
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | SERINE/THREONINE protein kinase | protein | 267 | 42% helix, 21% strand | A5TY84 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.78 | 0.84 | 71 | AGS, MN |
| 2 | 627 | 0.78 | 0.84 | 71 | AGS, MN |
| 3 | 584 | 0.77 | 0.83 | 73 | AGS, MN |
| 4 | 410 | 0.74 | 0.84 | 50 | AGS, MN |
| 5 | 367 | 0.64 | 0.79 | 47 | empty |
Interfaces
5 interfaces between chains.
- A–D · 484 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 449 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 385 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 332 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3ORI · Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 1) · 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 A5TY84
- Elsewhere: RCSB PDB 3ORI · PDBe 3ORI · UniProt A5TY84
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