Research workbench
Crystal structure of the C-terminal domain of a probable lysr family transcriptional regulator from rhodococcus sp. RHA1
Analyse Crystal structure of the C-terminal domain of a probable lysr family… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QL3
- Type
- protein
- Length
- 2,460 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable transcriptional regulator, lysr family protein
- UniProt
- Q0SFM8
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Probable transcriptional regulator, lysr family protein | protein | 205 | 31% helix, 31% strand | Q0SFM8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 76 copies · chains A, C, D, B, J, H, E, F, G, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.79 | 0.82 | 108 | PO4 |
| 2 | 302 | 0.74 | 0.86 | 56 | PO4 |
| 3 | 358 | 0.71 | 0.84 | 59 | PO4 |
| 4 | 382 | 0.71 | 0.83 | 58 | PO4 |
| 5 | 801 | 0.70 | 0.76 | 84 | PO4 |
Interfaces
23 interfaces between chains.
- C–D · 1513 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 1512 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1511 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 1485 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1473 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 2QL3 · Crystal structure of the C-terminal domain of a probable LysR family transcriptional… · 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 Q0SFM8
- Elsewhere: RCSB PDB 2QL3 · PDBe 2QL3 · UniProt Q0SFM8
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