Research workbench
Arginase from medicago truncatula in complex with ornithine
Analyse Arginase from medicago truncatula in complex with ornithine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VST
- Type
- protein
- Length
- 3,824 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase
- EC
- 3.5.3.1
- UniProt
- G7JFU5
- Ligands
- ORN, MN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Arginase (EC 3.5.3.1) | protein | 317 | 45% helix, 18% strand | G7JFU5 |
| B, C, J, K | Arginase (EC 3.5.3.1) | protein | 318 | 45% helix, 19% strand | G7JFU5 |
| D, F, G, H | Arginase (EC 3.5.3.1) | protein | 320 | 45% helix, 19% strand | G7JFU5 |
| E, L | Arginase (EC 3.5.3.1) | protein | 319 | 45% helix, 19% strand | G7JFU5 |
Ligands and binding sites
- ORN · L-ornithine · ligand · 7 copies · chains A, B, C, D, E, F, H, I, J, L, K
- MN · Manganese (II) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.89 | 0.90 | 129 | empty |
| 2 | 1087 | 0.89 | 0.90 | 131 | empty |
| 3 | 571 | 0.83 | 0.88 | 73 | empty |
| 4 | 527 | 0.83 | 0.89 | 56 | empty |
| 5 | 835 | 0.82 | 0.84 | 76 | empty |
Interfaces
28 interfaces between chains.
- C–F · 1714 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1690 Ų buried · 26 hydrogen bonds · protein-protein
- G–J · 1685 Ų buried · 31 hydrogen bonds · protein-protein
- I–L · 1683 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 1678 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6VST · Arginase from Medicago truncatula in complex with ornithine · the same entry in another collection · chain L against L, 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 G7JFU5
- Elsewhere: RCSB PDB 6VST · PDBe 6VST · UniProt G7JFU5
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