Research workbench
Crystal structure of the mycobacterium tuberculosis pknb kinase domain (L33E mutant) in complex with its substrate gara
Analyse Crystal structure of the mycobacterium tuberculosis pknb kinase domain (L33E… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I2P
- Type
- protein
- Length
- 761 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pknb; Glycogen accumulation regulator gara…
- EC
- 2.7.11.1
- UniProt
- P9WI81, P9WJA9
- Ligands
- ACP, MG, SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pknb (EC 2.7.11.1) | protein | 272 | 38% helix, 21% strand | P9WI81 |
| B | SERINE/THREONINE-protein kinase pknb (EC 2.7.11.1) | protein | 266 | 37% helix, 21% strand | P9WI81 |
| D | Glycogen accumulation regulator gara | protein | 114 | 3% helix, 43% strand | P9WJA9 |
| E | Glycogen accumulation regulator gara | protein | 104 | 0% helix, 46% strand | P9WJA9 |
| C | Unk-unk-unk-unk-unk | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.82 | 0.83 | 107 | ACP, MG |
| 2 | 623 | 0.78 | 0.84 | 79 | ACP, MG |
| 3 | 205 | 0.49 | 0.76 | 26 | empty |
| 4 | 138 | 0.46 | 0.77 | 23 | SO4 |
| 5 | 83 | 0.40 | 0.78 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1125 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 654 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 559 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 215 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 114 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6I2P · Crystal structure of the Mycobacterium tuberculosis PknB kinase domain (L33E mutant) in… · the same entry in another collection · chain C against C, TM-score 1.00
- P9WJA9 · AlphaFold monomer V2.0 prediction for glycogen accumulation regulator gara (P9WJA9) · a predicted model of the same protein · chain E against A, TM-score 0.94
- P9WI81 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pknb (P9WI81) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P9WI81
- Every structure of UniProt P9WJA9
- Elsewhere: RCSB PDB 6I2P · PDBe 6I2P · UniProt P9WI81 · UniProt P9WJA9
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