Research workbench
Crystal structure of putative transcriptional regulator containing a luxr DNA binding domain (NP_811094.1) from bacteroides thetaiotaomicron vpi-5482 at 2.04 a resolution
Analyse Crystal structure of putative transcriptional regulator containing a luxr DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CLO
- Type
- protein
- Length
- 773 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator
- UniProt
- Q8A5Q7
- Ligands
- NA, CL
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transcriptional regulator | protein | 258 | 42% helix, 22% strand | Q8A5Q7 |
| C | Transcriptional regulator | protein | 257 | 45% helix, 21% strand | Q8A5Q7 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains C
- CL · Chloride ion · ion · 7 copies · chains A, B, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.85 | 0.93 | 45 | CL |
| 2 | 305 | 0.55 | 0.76 | 37 | empty |
| 3 | 85 | 0.55 | 0.85 | 19 | empty |
| 4 | 159 | 0.53 | 0.79 | 22 | empty |
| 5 | 119 | 0.42 | 0.76 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1408 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 297 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 3CLO · Crystal structure of putative transcriptional regulator containing a LuxR DNA binding… · 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 Q8A5Q7
- Elsewhere: RCSB PDB 3CLO · PDBe 3CLO · UniProt Q8A5Q7
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