Research workbench
Crystal structure of the binuclear manganese metalloenzyme arginase complexed with 2(S)-amino-6-boronohexanoic acid, an L-arginine analog
Analyse Crystal structure of the binuclear manganese metalloenzyme arginase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D3V
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (arginase)
- EC
- 3.5.3.1
- UniProt
- P07824
- Ligands
- ABH, MN
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (arginase) (EC 3.5.3.1) | protein | 308 | 42% helix, 16% strand | P07824 |
Ligands and binding sites
- ABH · 2(S)-amino-6-boronohexanoic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.49 | 0.83 | 21 | ABH |
| 2 | 85 | 0.46 | 0.81 | 16 | empty |
| 3 | 94 | 0.46 | 0.81 | 22 | ABH |
| 4 | 82 | 0.43 | 0.79 | 14 | empty |
Compared structures
- 1D3V · Crystal structure of the binuclear manganese metalloenzyme arginase complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- P07824 · AlphaFold monomer V2.0 prediction for arginase-1 (P07824) · a predicted model of the same protein · chain B against A, 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 P07824
- Elsewhere: RCSB PDB 1D3V · PDBe 1D3V · UniProt P07824
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