MolNFT v1 · #157953 · protein
1.7 ångström resolution crystal structure of arginase from bacillus subtilis subsp. subtilis str. 168
6NFP: “1.7 ångström resolution crystal structure of arginase from bacillus subtilis subsp. subtilis str. 168”. X-ray diffraction, 6 ligands (URE, GOA, MG), 20 pockets (best druggability 0.81). MolNFT v1 #157953 on GenesisL1: 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
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