MolNFT v1 · #150030 · protein
Crystal structure of spx in complex with yjbh
6GHO · Regulatory protein spx: “Crystal structure of spx in complex with yjbh”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.75). MolNFT v1 #150030 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GHO
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein spx; UPF0413 protein GK0824
- UniProt
- O31602, Q5L1S1
- Ligands
- CL
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulatory protein spx | protein | 126 | 35% helix, 17% strand | O31602 |
| B | UPF0413 protein GK0824 | protein | 274 | 55% helix, 14% strand | Q5L1S1 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.75 | 0.80 | 66 | empty |
| 2 | 59 | 0.64 | 0.93 | 23 | empty |
| 3 | 104 | 0.53 | 0.83 | 21 | empty |
| 4 | 135 | 0.50 | 0.79 | 16 | empty |
| 5 | 69 | 0.36 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1692 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6GHO · Crystal structure of Spx in complex with YjbH · the same entry in another collection · chain A against A, TM-score 1.00
- Q5L1S1 · AlphaFold monomer V2.0 prediction for clpxp adapter protein spxh (Q5L1S1) · a predicted model of the same protein · chain B against A, TM-score 0.98
- O31602 · AlphaFold monomer V2.0 prediction for global transcriptional regulator spx (O31602) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 O31602
- Every structure of UniProt Q5L1S1
- Elsewhere: RCSB PDB 6GHO · PDBe 6GHO · UniProt O31602 · UniProt Q5L1S1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.