Research workbench
1.7 ångström resolution crystal structure of arginase from bacillus subtilis subsp. subtilis str. 168
Analyse 1.7 ångström resolution crystal structure of arginase from bacillus subtilis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NFP
- Type
- protein
- Length
- 1,737 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase
- EC
- 3.5.3.1
- UniProt
- P39138
- Ligands
- URE, GOA, MG, NA, SO4, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginase (EC 3.5.3.1) | protein | 292 | 44% helix, 18% strand | P39138 |
| B | Arginase (EC 3.5.3.1) | protein | 290 | 45% helix, 19% strand | P39138 |
| C | Arginase (EC 3.5.3.1) | protein | 290 | 43% helix, 19% strand | P39138 |
| D | Arginase (EC 3.5.3.1) | protein | 289 | 45% helix, 19% strand | P39138 |
| E | Arginase (EC 3.5.3.1) | protein | 287 | 45% helix, 19% strand | P39138 |
| F | Arginase (EC 3.5.3.1) | protein | 289 | 45% helix, 19% strand | P39138 |
Ligands and binding sites
- URE · Urea · ligand · 16 copies · chains A, B, C, D, E, F
- GOA · Glycolic acid · ligand · 4 copies · chains B, C, D, F
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 3 copies · chains A, D, B, C, E, F
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, F, D, E
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D, E
- FMT · Formic acid · additive · 15 copies · chains A, B, D, C, E, F
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, D, E, C, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.81 | 0.82 | 86 | FMT |
| 2 | 870 | 0.80 | 0.82 | 72 | empty |
| 3 | 743 | 0.74 | 0.79 | 52 | CL, EDO |
| 4 | 642 | 0.70 | 0.78 | 49 | CL, GOA |
| 5 | 515 | 0.67 | 0.78 | 49 | empty |
Interfaces
12 interfaces between chains.
- A–D · 780 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 758 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 739 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 701 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 699 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6NFP · 1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp.… · the same entry in another collection · chain F against F, TM-score 1.00
- P39138 · AlphaFold monomer V2.0 prediction for arginase (P39138) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P39138
- Elsewhere: RCSB PDB 6NFP · PDBe 6NFP · UniProt P39138
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.