Research workbench
Arginase from bacillus caldevelox, L-lysine complex
Analyse Arginase from bacillus caldevelox, L-lysine complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CEV
- Type
- protein
- Length
- 1,788 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (arginase)
- EC
- 3.5.3.1
- UniProt
- P53608
- Ligands
- LYS, GAI, MN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Protein (arginase) (EC 3.5.3.1) | protein | 298 | 45% helix, 17% strand | P53608 |
Ligands and binding sites
- LYS · Lysine · ligand · 6 copies · chains A, B, C, D, E, F
- GAI · Guanidine · ligand · 6 copies · chains A, B, C, D, F, E
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.76 | 0.80 | 61 | empty |
| 2 | 1070 | 0.76 | 0.78 | 69 | empty |
| 3 | 136 | 0.57 | 0.83 | 22 | GAI |
| 4 | 185 | 0.56 | 0.80 | 23 | GAI |
| 5 | 163 | 0.55 | 0.81 | 25 | GAI |
Interfaces
7 interfaces between chains.
- A–B · 701 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 684 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 682 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 678 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 667 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- P53608 · AlphaFold monomer V2.0 prediction for arginase (P53608) · a predicted model of the same protein · chain C 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 P53608
- Elsewhere: RCSB PDB 5CEV · PDBe 5CEV · UniProt P53608
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