Research workbench
Crystal structure of protein kinase pkng from mycobacterium tuberculosis in complex with tetrahydrobenzothiophene AX20017
Analyse Crystal structure of protein kinase pkng from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PZI
- Type
- protein
- Length
- 1,298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable SERINE/THREONINE-protein kinase pkng
- EC
- 2.7.11.1
- UniProt
- P65728
- Ligands
- AXX, CD, CL
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable SERINE/THREONINE-protein kinase pkng (EC 2.7.11.1) | protein | 654 | 48% helix, 13% strand | P65728 |
| B | Probable SERINE/THREONINE-protein kinase pkng (EC 2.7.11.1) | protein | 644 | 44% helix, 13% strand | P65728 |
Ligands and binding sites
- AXX · 2-[(cyclopropylcarbonyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.80 | 0.82 | 90 | AXX |
| 2 | 1010 | 0.77 | 0.79 | 82 | empty |
| 3 | 478 | 0.76 | 0.84 | 59 | empty |
| 4 | 406 | 0.72 | 0.83 | 48 | GOL |
| 5 | 415 | 0.72 | 0.83 | 48 | GOL |
Interfaces
1 interface between chains.
- A–B · 1319 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2PZI · Crystal Structure of Protein kinase PknG from Mycobacterium tuberculosis in Complex with… · 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 P65728
- Elsewhere: RCSB PDB 2PZI · PDBe 2PZI · UniProt P65728
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