MolNFT v1 · #150019 · protein
Crystal structure of spx in complex with yjbh (oxidized)
6GHB · Regulatory protein spx: “Crystal structure of spx in complex with yjbh (oxidized)”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.76). MolNFT v1 #150019 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6GHB
- Type
- protein
- Length
- 769 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein spx; UPF0413 protein GK0824
- UniProt
- O31602, Q5L1S1
- Ligands
- MG
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulatory protein spx | protein | 116 | 34% helix, 18% strand | O31602 |
| B | UPF0413 protein GK0824 | protein | 263 | 52% helix, 15% strand | Q5L1S1 |
| C | Regulatory protein spx | protein | 123 | 31% helix, 17% strand | O31602 |
| D | UPF0413 protein GK0824 | protein | 267 | 52% helix, 14% strand | Q5L1S1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.76 | 0.81 | 58 | empty |
| 2 | 618 | 0.73 | 0.80 | 57 | empty |
| 3 | 81 | 0.50 | 0.84 | 20 | empty |
| 4 | 83 | 0.48 | 0.82 | 22 | empty |
| 5 | 66 | 0.42 | 0.81 | 21 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1673 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1545 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6GHB · Crystal structure of Spx in complex with YjbH (oxidized) · the same entry in another collection · chain D against D, 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 0.99
- O31602 · AlphaFold monomer V2.0 prediction for global transcriptional regulator spx (O31602) · a predicted model of the same protein · chain C against A, TM-score 0.88
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 6GHB · PDBe 6GHB · UniProt O31602 · UniProt Q5L1S1
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