Research workbench
Crystal structure of mycobacterium tuberculosis H37RV pknf kinase domain
Analyse Crystal structure of mycobacterium tuberculosis H37RV pknf kinase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NAA
- Type
- protein
- Length
- 937 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-specific SERINE/THREONINE protein kinase
- EC
- 2.7.11.1
- UniProt
- A0A045H1A5
- Ligands
- V17
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-specific SERINE/THREONINE protein kinase (EC 2.7.11.1) | protein | 244 | 39% helix, 20% strand | A0A045H1A5 |
| B | Non-specific SERINE/THREONINE protein kinase (EC 2.7.11.1) | protein | 242 | 38% helix, 20% strand | A0A045H1A5 |
| C | Non-specific SERINE/THREONINE protein kinase (EC 2.7.11.1) | protein | 217 | 43% helix, 14% strand | A0A045H1A5 |
| D | Non-specific SERINE/THREONINE protein kinase (EC 2.7.11.1) | protein | 234 | 40% helix, 19% strand | A0A045H1A5 |
Ligands and binding sites
- V17 · (4-{[4-(1-benzothiophen-2-yl)pyrimidin-2-yl]amino}phenyl)[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.78 | 0.80 | 97 | empty |
| 2 | 341 | 0.67 | 0.81 | 60 | empty |
| 3 | 296 | 0.63 | 0.80 | 40 | V17 |
| 4 | 199 | 0.56 | 0.80 | 33 | empty |
| 5 | 144 | 0.56 | 0.82 | 21 | V17 |
Interfaces
4 interfaces between chains.
- A–B · 1106 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1067 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 359 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 220 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7NAA · Crystal structure of Mycobacterium tuberculosis H37Rv PknF kinase domain · 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 A0A045H1A5
- Elsewhere: RCSB PDB 7NAA · PDBe 7NAA · UniProt A0A045H1A5
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