MolNFT v1 · #122714 · protein
Structure of P. vulgaris higb toxin Y91A variant
5IXL · Endoribonuclease higb: “Structure of P. vulgaris higb toxin Y91A variant”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.82). MolNFT v1 #122714 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IXL
- Type
- protein
- Length
- 763 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease higb
- EC
- 3.1.-.-
- UniProt
- Q7A225
- Ligands
- CL
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease higb (EC 3.1.-.-) | protein | 99 | 41% helix, 28% strand | Q7A225 |
| B, E, G | Endoribonuclease higb (EC 3.1.-.-) | protein | 98 | 39% helix, 30% strand | Q7A225 |
| C, F, H | Endoribonuclease higb (EC 3.1.-.-) | protein | 92 | 38% helix, 30% strand | Q7A225 |
| D | Endoribonuclease higb (EC 3.1.-.-) | protein | 94 | 40% helix, 29% strand | Q7A225 |
Ligands and binding sites
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.82 | 0.90 | 71 | empty |
| 2 | 103 | 0.64 | 0.89 | 30 | empty |
| 3 | 70 | 0.56 | 0.89 | 18 | empty |
| 4 | 51 | 0.52 | 0.89 | 13 | empty |
| 5 | 130 | 0.49 | 0.80 | 23 | empty |
Interfaces
17 interfaces between chains.
- A–H · 502 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 444 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 366 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 353 Ų buried · 4 hydrogen bonds · protein-protein
- A–G · 309 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 Q7A225
- Elsewhere: RCSB PDB 5IXL · PDBe 5IXL · UniProt Q7A225
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