MolNFT v1 · #27888 · protein
C-terminal domain of escherichia COLI arginine repressor/ L- arginine complex; pb derivative
1XXA: “C-terminal domain of escherichia COLI arginine repressor/ L- arginine complex; pb derivative”. X-ray diffraction, 2 ligands (ARG, PB), 6 pockets (best druggability 0.82). MolNFT v1 #27888 on GenesisL1: 3D structure, binding sites…
- PDB
- 1XXA
- Type
- protein
- Length
- 429 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine repressor
- UniProt
- P0A6D0
- Ligands
- ARG, PB
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Arginine repressor | protein | 71 | 24% helix, 32% strand | P0A6D0 |
| B | Arginine repressor | protein | 72 | 31% helix, 32% strand | P0A6D0 |
| C | Arginine repressor | protein | 73 | 36% helix, 32% strand | P0A6D0 |
Ligands and binding sites
- ARG · Arginine · ligand · 6 copies · chains A, C, D, B, F, E
- PB · Lead (II) ion · metal · 4 copies · chains B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.82 | 0.92 | 38 | empty |
| 2 | 127 | 0.55 | 0.83 | 26 | ARG |
| 3 | 138 | 0.52 | 0.81 | 34 | ARG |
| 4 | 56 | 0.30 | 0.76 | 15 | empty |
| 5 | 60 | 0.28 | 0.73 | 17 | empty |
Interfaces
12 interfaces between chains.
- D–F · 591 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 575 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 558 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 516 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1XXA · C-terminal domain of escherichia COLI arginine repressor/ L-arginine complex; pb… · the same entry in another collection · chain E against E, 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 1XXA · PDBe 1XXA · UniProt P0A6D0
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