Research workbench
Structure of C406A arginine deiminase in complex with L-arginine
Analyse Structure of C406A arginine deiminase in complex with L-arginine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A9G
- Type
- protein
- Length
- 1,618 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
- Ligands
- ARG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine deiminase (EC 3.5.3.6) | protein | 405 | 36% helix, 21% strand | P13981 |
| B | Arginine deiminase (EC 3.5.3.6) | protein | 405 | 36% helix, 23% strand | P13981 |
| C | Arginine deiminase (EC 3.5.3.6) | protein | 402 | 34% helix, 21% strand | P13981 |
| D | Arginine deiminase (EC 3.5.3.6) | protein | 406 | 35% helix, 21% strand | P13981 |
Ligands and binding sites
- ARG · Arginine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.80 | 0.96 | 22 | empty |
| 2 | 135 | 0.78 | 0.96 | 20 | empty |
| 3 | 711 | 0.77 | 0.82 | 56 | empty |
| 4 | 486 | 0.76 | 0.84 | 53 | empty |
| 5 | 532 | 0.75 | 0.83 | 48 | ARG |
Interfaces
4 interfaces between chains.
- A–D · 1907 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1715 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1043 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1024 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 2A9G · PDBe 2A9G · UniProt P13981
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