MolNFT v1 · #104213 · protein
Crystal structure of schistosoma mansoni arginase in complex with inhibitor abhdp
4Q3R: “Crystal structure of schistosoma mansoni arginase in complex with inhibitor abhdp”. X-ray diffraction, 4 ligands (XA2, CS, MN), 8 pockets (best druggability 0.71). MolNFT v1 #104213 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4Q3R
- Type
- protein
- Length
- 1,316 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
- XA2, CS, MN, CL
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 4 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 | Arginase (EC 3.5.3.1) | protein | 333 | 42% helix, 16% strand | Q6WVP6 |
| C | Arginase (EC 3.5.3.1) | protein | 333 | 42% helix, 15% strand | Q6WVP6 |
| D | Arginase (EC 3.5.3.1) | protein | 314 | 40% helix, 16% strand | Q6WVP6 |
Ligands and binding sites
- XA2 · (R)-2-amino-6-borono-2-(1-(3,4-dichlorobenzyl)piperidin-4-yl)hexanoic acid · ligand · 4 copies · chains A, B, C, D
- CS · Cesium ion · metal · 11 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B, C
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.71 | 0.83 | 28 | empty |
| 2 | 101 | 0.46 | 0.80 | 25 | XA2 |
| 3 | 97 | 0.44 | 0.80 | 23 | XA2 |
| 4 | 94 | 0.43 | 0.79 | 20 | XA2 |
| 5 | 89 | 0.41 | 0.79 | 19 | XA2 |
Interfaces
3 interfaces between chains.
- A–B · 271 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 261 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4Q3R · Crystal structure of Schistosoma mansoni arginase in complex with inhibitor ABHDP · 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 4Q3R · PDBe 4Q3R · UniProt Q6WVP6
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