Research workbench
Crystal structure of the arginine repressor from mycobacterium tuberculosis bound with its DNA operator and co-repressor, L-arginine
Analyse Crystal structure of the arginine repressor from mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FHZ
- Type
- protein + DNA
- Length
- 1,072 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine repressor; 5'-D(*TP*GP*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*AP…
- UniProt
- P0A4Y8
- Ligands
- ARG
- Pockets
- 17 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Arginine repressor | protein | 155 | 40% helix, 19% strand | P0A4Y8 |
| B | Arginine repressor | protein | 161 | 40% helix, 19% strand | P0A4Y8 |
| C | Arginine repressor | protein | 160 | 40% helix, 19% strand | P0A4Y8 |
| D | Arginine repressor | protein | 166 | 39% helix, 19% strand | P0A4Y8 |
| G, I, K | 5'-D(*TP*GP*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*AP *AP*A)-3' | dna | 20 | — | — |
| H, J, L | 5'-D(*TP*TP*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*AP *CP*A)-3' | dna | 20 | — | — |
Ligands and binding sites
- ARG · Arginine · ligand · 9 copies · chains A, C, F, B, E, D
- ACT · Acetate ion · additive · 2 copies · chains A, D, L, B, E
- GOL · Glycerol · additive · chains C, D, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.89 | 0.91 | 155 | ARG, GOL |
| 2 | 804 | 0.82 | 0.85 | 83 | ARG, ACT |
| 3 | 223 | 0.79 | 0.93 | 34 | ARG |
| 4 | 313 | 0.75 | 0.87 | 35 | empty |
| 5 | 314 | 0.74 | 0.87 | 36 | empty |
Interfaces
34 interfaces between chains.
- A–D · 1252 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 1202 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1195 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1190 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 910 Ų buried · 80 hydrogen bonds · nucleic-nucleic
Compared structures
- 3FHZ · Crystal structure of the arginine repressor from Mycobacterium tuberculosis bound 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 P0A4Y8
- Elsewhere: RCSB PDB 3FHZ · PDBe 3FHZ · UniProt P0A4Y8
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