MolNFT v1 · #167705 · protein
Arginase from arabidopsis thaliana in complex with ornithine
6VSU · Arginase 1, mitochondrial: “Arginase from arabidopsis thaliana in complex with ornithine”. X-ray diffraction, 3 ligands (ORN, MN, NA), 20 pockets (best druggability 0.89). MolNFT v1 #167705 on GenesisL1: 3D structure, binding sites…
- PDB
- 6VSU
- Type
- protein
- Length
- 7,593 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase 1, mitochondrial
- EC
- 3.5.3.1, 3.5.3.11
- UniProt
- P46637
- Ligands
- ORN, MN, NA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G, I, K, M, N, O, P, Q, R, S, U, V, X | Arginase 1, mitochondrial (EC 3.5.3.1, 3.5.3.11) | protein | 316 | 46% helix, 18% strand | P46637 |
| B, H, J, L, W | Arginase 1, mitochondrial (EC 3.5.3.1, 3.5.3.11) | protein | 317 | 46% helix, 18% strand | P46637 |
| E, T | Arginase 1, mitochondrial (EC 3.5.3.1, 3.5.3.11) | protein | 318 | 46% helix, 18% strand | P46637 |
Ligands and binding sites
- ORN · L-ornithine · ligand · 9 copies · chains A, B, C, D, E, F, G, I, J, K, P, R, S, U, V, X
- MN · Manganese (II) ion · metal · 48 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- NA · Sodium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- GOL · Glycerol · additive · 30 copies · chains B, C, A, F, D, E, G, H, I, J, K, L, M, N, P, Q, R, S, T, U, W, X
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains G, I, K, L, U
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 | 947 | 0.89 | 0.91 | 112 | empty |
| 2 | 1101 | 0.89 | 0.90 | 133 | empty |
| 3 | 733 | 0.88 | 0.91 | 96 | GOL |
| 4 | 739 | 0.87 | 0.91 | 97 | empty |
| 5 | 772 | 0.81 | 0.84 | 82 | empty |
Interfaces
57 interfaces between chains.
- A–D · 1320 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1309 Ų buried · 14 hydrogen bonds · protein-protein
- I–L · 1308 Ų buried · 16 hydrogen bonds · protein-protein
- T–W · 1308 Ų buried · 17 hydrogen bonds · protein-protein
- H–K · 1285 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6VSU · Arginase from Arabidopsis thaliana in Complex with Ornithine · the same entry in another collection · chain C against C, 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 P46637
- Elsewhere: RCSB PDB 6VSU · PDBe 6VSU · UniProt P46637
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