MolNFT v1 · #104224 · protein
Crystal structure of schistosoma mansoni arginase in complex with L- ornithine
4Q42: “Crystal structure of schistosoma mansoni arginase in complex with L- ornithine”. X-ray diffraction, 2 ligands (ORN, MN), 9 pockets (best druggability 0.72). MolNFT v1 #104224 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4Q42
- Type
- protein
- Length
- 1,337 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase
- EC
- 3.5.3.1
- UniProt
- Q6WVP6
- Ligands
- ORN, MN
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginase (EC 3.5.3.1) | protein | 336 | 41% helix, 16% strand | Q6WVP6 |
| B, C | Arginase (EC 3.5.3.1) | protein | 335 | 42% helix, 16% strand | Q6WVP6 |
| D | Arginase (EC 3.5.3.1) | protein | 331 | 40% helix, 17% strand | Q6WVP6 |
Ligands and binding sites
- ORN · L-ornithine · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · 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 | 497 | 0.72 | 0.81 | 46 | empty |
| 2 | 139 | 0.44 | 0.76 | 27 | empty |
| 3 | 83 | 0.43 | 0.80 | 20 | ORN |
| 4 | 98 | 0.43 | 0.79 | 18 | ORN |
| 5 | 90 | 0.43 | 0.80 | 20 | ORN |
Interfaces
3 interfaces between chains.
- A–B · 259 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Q42 · Crystal structure of Schistosoma mansoni arginase in complex with L-ornithine · the same entry in another collection · chain B against B, 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 Q6WVP6
- Elsewhere: RCSB PDB 4Q42 · PDBe 4Q42 · UniProt Q6WVP6
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