MolNFT v1 · #161085 · protein
Complex of arginase 2 with example 23
6Q37 · Arginase-2, mitochondrial: “Complex of arginase 2 with example 23”. X-ray diffraction, 3 ligands (BEN, HE8, MN), 9 pockets (best druggability 0.80). MolNFT v1 #161085 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Q37
- Type
- protein
- Length
- 918 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase-2, mitochondrial
- EC
- 3.5.3.1
- UniProt
- P78540
- Ligands
- BEN, HE8, MN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginase-2, mitochondrial (EC 3.5.3.1) | protein | 306 | 43% helix, 18% strand | P78540 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 3 copies · chains A, B, C
- HE8 · 3-[(3~{S},4~{R})-4-azanyl-4-carboxy-pyrrolidin-3-yl]propyl-tris(oxidanyl)boranuide · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.80 | 0.81 | 67 | EDO |
| 2 | 118 | 0.49 | 0.81 | 23 | HE8 |
| 3 | 95 | 0.47 | 0.81 | 20 | empty |
| 4 | 111 | 0.46 | 0.79 | 23 | HE8 |
| 5 | 98 | 0.45 | 0.80 | 22 | HE8 |
Interfaces
3 interfaces between chains.
- A–B · 687 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 682 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 668 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
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 P78540
- Elsewhere: RCSB PDB 6Q37 · PDBe 6Q37 · UniProt P78540
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