MolNFT v1 · #27889 · protein
C-terminal domain of escherichia COLI arginine repressor/ L-arginine complex
1XXB: “C-terminal domain of escherichia COLI arginine repressor/ L-arginine complex”. X-ray diffraction, 1 ligand (ARG), 7 pockets (best druggability 0.82). MolNFT v1 #27889 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XXB
- Type
- protein
- Length
- 428 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine repressor
- UniProt
- P0A6D0
- Ligands
- ARG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Arginine repressor | protein | 71 | 35% helix, 27% strand | P0A6D0 |
| B, C | Arginine repressor | protein | 72 | 35% helix, 32% strand | P0A6D0 |
Ligands and binding sites
- ARG · Arginine · ligand · 6 copies · chains A, C, D, B, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.82 | 0.91 | 41 | empty |
| 2 | 105 | 0.53 | 0.83 | 27 | ARG |
| 3 | 145 | 0.52 | 0.80 | 26 | ARG |
| 4 | 56 | 0.44 | 0.84 | 15 | ARG |
| 5 | 50 | 0.43 | 0.84 | 16 | ARG |
Interfaces
12 interfaces between chains.
- D–F · 563 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 536 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 517 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 515 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1XXB · C-terminal domain of escherichia COLI arginine repressor/ L-arginine complex · the same entry in another collection · chain B against B, TM-score 1.00
- P0A6D0 · AlphaFold monomer V2.0 prediction for arginine repressor (P0A6D0) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 P0A6D0
- Elsewhere: RCSB PDB 1XXB · PDBe 1XXB · UniProt P0A6D0
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