Research workbench
Crystal structure of the oligomerization domain hexamer of the arginine repressor protein from mycobacterium tuberculosis in complex with 9 arginines.
Analyse Crystal structure of the oligomerization domain hexamer of the arginine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CAG
- Type
- protein
- Length
- 468 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine repressor
- UniProt
- P0A4Y8
- Ligands
- ARG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine repressor | protein | 77 | 42% helix, 29% strand | P0A4Y8 |
| B, C, E | Arginine repressor | protein | 79 | 41% helix, 28% strand | P0A4Y8 |
| D | Arginine repressor | protein | 78 | 42% helix, 28% strand | P0A4Y8 |
| F | Arginine repressor | protein | 76 | 39% helix, 29% strand | P0A4Y8 |
Ligands and binding sites
- ARG · Arginine · ligand · 9 copies · chains A, C, F, B, E, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.78 | 0.91 | 32 | ARG |
| 2 | 167 | 0.58 | 0.82 | 30 | ARG |
| 3 | 173 | 0.57 | 0.82 | 29 | ARG |
| 4 | 149 | 0.55 | 0.82 | 33 | ARG |
| 5 | 50 | 0.31 | 0.77 | 15 | empty |
Interfaces
12 interfaces between chains.
- E–F · 532 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 512 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 496 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 479 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3CAG · Crystal structure of the oligomerization domain hexamer of the arginine repressor protein… · the same entry in another collection · chain E against E, 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 3CAG · PDBe 3CAG · UniProt P0A4Y8
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