Research workbench
Crystal structure of helicobacter pylori arginase
Analyse Crystal structure of helicobacter pylori arginase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G3H
- Type
- protein
- Length
- 1,216 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase (rocf)
- UniProt
- O25949
- Ligands
- MN
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginase (rocf) | protein | 301 | 46% helix, 18% strand | O25949 |
| B | Arginase (rocf) | protein | 305 | 46% helix, 18% strand | O25949 |
| C | Arginase (rocf) | protein | 310 | 46% helix, 17% strand | O25949 |
| D | Arginase (rocf) | protein | 300 | 46% helix, 17% strand | O25949 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.82 | 0.84 | 77 | empty |
| 2 | 893 | 0.82 | 0.84 | 81 | empty |
| 3 | 196 | 0.68 | 0.86 | 32 | empty |
| 4 | 306 | 0.62 | 0.79 | 43 | empty |
| 5 | 205 | 0.59 | 0.81 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–D · 689 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 608 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 603 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 345 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 336 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4G3H · Crystal structure of helicobacter pylori arginase · the same entry in another collection · chain A against A, 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 O25949
- Elsewhere: RCSB PDB 4G3H · PDBe 4G3H · UniProt O25949
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.