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Structure of D280A arginine deiminase with L-arginine forming a S- alkylthiouronium reaction intermediate
Analyse Structure of D280A arginine deiminase with L-arginine forming a S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ABR
- Type
- protein
- Length
- 1,613 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine deiminase
- EC
- 3.5.3.6
- UniProt
- P13981
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine deiminase (EC 3.5.3.6) | protein | 402 | 38% helix, 22% strand | P13981 |
| B | Arginine deiminase (EC 3.5.3.6) | protein | 406 | 35% helix, 22% strand | P13981 |
| C | Arginine deiminase (EC 3.5.3.6) | protein | 403 | 33% helix, 22% strand | P13981 |
| D | Arginine deiminase (EC 3.5.3.6) | protein | 402 | 37% helix, 20% strand | P13981 |
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.84 | 0.85 | 108 | empty |
| 2 | 1016 | 0.83 | 0.84 | 99 | empty |
| 3 | 924 | 0.78 | 0.81 | 82 | empty |
| 4 | 119 | 0.78 | 0.96 | 22 | empty |
| 5 | 95 | 0.76 | 0.97 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1899 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1773 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1036 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1028 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 2ABR · Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium… · the same entry in another collection · chain D against D, TM-score 1.00
- P13981 · AlphaFold monomer V2.0 prediction for arginine deiminase (P13981) · a predicted model of the same protein · chain D 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 P13981
- Elsewhere: RCSB PDB 2ABR · PDBe 2ABR · UniProt P13981
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