MolNFT v1 · #48638 · protein
Crystal structure of protein kinase pkng from mycobacterium tuberculosis in complex with tetrahydrobenzothiophene AX20017
2PZI · Probable SERINE/THREONINE-protein kinase pkng: “Crystal structure of protein kinase pkng from mycobacterium tuberculosis in complex with…”. X-ray diffraction, 3 ligands (AXX, CD, CL), 17 pockets (best druggability 0.80). MolNFT v1…
- 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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