Research workbench
Extracellular domain of mycobacterium tuberculosis pknd
Analyse Extracellular domain of mycobacterium tuberculosis pknd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RWI
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pknd
- EC
- 2.7.1.37
- UniProt
- O05871
- Ligands
- CD
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | SERINE/THREONINE-protein kinase pknd (EC 2.7.1.37) | protein | 254 | 5% helix, 40% strand | O05871 |
| A | SERINE/THREONINE-protein kinase pknd (EC 2.7.1.37) | protein | 256 | 5% helix, 41% strand | O05871 |
Ligands and binding sites
- CD · Cadmium ion · metal · 14 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.76 | 0.84 | 52 | empty |
| 2 | 434 | 0.74 | 0.84 | 43 | empty |
| 3 | 216 | 0.61 | 0.82 | 37 | CD |
| 4 | 81 | 0.36 | 0.76 | 18 | empty |
| 5 | 68 | 0.34 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 597 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1RWI · Extracellular domain of Mycobacterium tuberculosis PknD · the same entry in another collection · chain B against B, 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 O05871
- Elsewhere: RCSB PDB 1RWI · PDBe 1RWI · UniProt O05871
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.