MolNFT v1 · #104222 · protein
Crystal structure of schistosoma mansoni arginase in complex with L- valine
4Q40: “Crystal structure of schistosoma mansoni arginase in complex with L- valine”. X-ray diffraction, 2 ligands (VAL, MN), 9 pockets (best druggability 0.73). MolNFT v1 #104222 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4Q40
- Type
- protein
- Length
- 1,336 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
- VAL, MN
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginase (EC 3.5.3.1) | protein | 335 | 41% helix, 16% strand | Q6WVP6 |
| D | Arginase (EC 3.5.3.1) | protein | 331 | 41% helix, 17% strand | Q6WVP6 |
Ligands and binding sites
- VAL · Valine · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C
- IMD · Imidazole · additive · 7 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 | 511 | 0.73 | 0.82 | 48 | empty |
| 2 | 88 | 0.45 | 0.81 | 21 | VAL |
| 3 | 91 | 0.44 | 0.80 | 23 | VAL |
| 4 | 122 | 0.43 | 0.77 | 24 | empty |
| 5 | 81 | 0.41 | 0.79 | 20 | VAL |
Interfaces
3 interfaces between chains.
- A–B · 269 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 246 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Q40 · Crystal structure of Schistosoma mansoni arginase in complex with L-valine · 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 4Q40 · PDBe 4Q40 · UniProt Q6WVP6
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