Research workbench
Crystal structure of arginine deiminase covalently linked with L-citrulline
Analyse Crystal structure of arginine deiminase covalently linked with L-citrulline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LXY
- Type
- protein
- Length
- 818 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine deiminase
- EC
- 3.5.3.6
- UniProt
- P23793
- Ligands
- CIR
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Arginine deiminase (EC 3.5.3.6) | protein | 409 | 37% helix, 21% strand | P23793 |
Ligands and binding sites
- CIR · Citrulline · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.58 | 0.84 | 22 | TRS |
| 2 | 128 | 0.57 | 0.84 | 22 | TRS |
| 3 | 205 | 0.49 | 0.76 | 31 | empty |
| 4 | 70 | 0.41 | 0.80 | 17 | empty |
| 5 | 52 | 0.31 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1300 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1LXY · Crystal Structure of Arginine Deiminase covalently linked with L-citrulline · the same entry in another collection · chain A against A, TM-score 1.00
- P23793 · AlphaFold monomer V2.0 prediction for arginine deiminase (P23793) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P23793
- Elsewhere: RCSB PDB 1LXY · PDBe 1LXY · UniProt P23793
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