Research workbench
Crystal structure of arginine deiminase covalently linked with a reaction intermediate
Analyse Crystal structure of arginine deiminase covalently linked with a reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S9R
- 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
- ARG, UNX
- Pockets
- 6 · best druggability 0.60
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
- ARG · Arginine · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 9 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
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 | 133 | 0.60 | 0.85 | 22 | TRS |
| 2 | 125 | 0.60 | 0.85 | 21 | TRS |
| 3 | 271 | 0.54 | 0.76 | 50 | empty |
| 4 | 113 | 0.42 | 0.77 | 15 | UNX |
| 5 | 66 | 0.38 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1355 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1S9R · Crystal structure of arginine deiminase covalently linked with a reaction intermediate · 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 B 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 1S9R · PDBe 1S9R · UniProt P23793
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