Research workbench
Crystal structure of arginine deiminase from mycoplasma penetrans
Analyse Crystal structure of arginine deiminase from mycoplasma penetrans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E4J
- Type
- protein
- Length
- 4,788 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine deiminase
- UniProt
- Q8EVF6
- Ligands
- CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Arginine deiminase | protein | 399 | 35% helix, 22% strand | Q8EVF6 |
Ligands and binding sites
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.85 | 0.88 | 96 | empty |
| 2 | 970 | 0.84 | 0.85 | 100 | empty |
| 3 | 870 | 0.74 | 0.78 | 83 | empty |
| 4 | 857 | 0.74 | 0.78 | 87 | empty |
| 5 | 831 | 0.74 | 0.78 | 80 | empty |
Interfaces
18 interfaces between chains.
- C–D · 1135 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1121 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1119 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1115 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 1113 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4E4J · Crystal structure of arginine deiminase from Mycoplasma penetrans · the same entry in another collection · chain C against C, TM-score 1.00
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 Q8EVF6
- Elsewhere: RCSB PDB 4E4J · PDBe 4E4J · UniProt Q8EVF6
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