Research workbench
Structure of four truncated and mutated forms of quenching protein
Analyse Structure of four truncated and mutated forms of quenching protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DJL
- Type
- protein
- Length
- 1,416 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein suppressor of quenching 1, chloroplastic
- EC
- 3.1.3.-
- UniProt
- Q8VZ10
- Ligands
- NA, CL
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Protein suppressor of quenching 1, chloroplastic (EC 3.1.3.-) | protein | 473 | 5% helix, 48% strand | Q8VZ10 |
| A | Protein suppressor of quenching 1, chloroplastic (EC 3.1.3.-) | protein | 473 | 6% helix, 48% strand | Q8VZ10 |
| B | Protein suppressor of quenching 1, chloroplastic (EC 3.1.3.-) | protein | 470 | 4% helix, 49% strand | Q8VZ10 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.81 | 0.82 | 95 | empty |
| 2 | 1062 | 0.77 | 0.79 | 77 | NA |
| 3 | 533 | 0.74 | 0.82 | 44 | empty |
| 4 | 303 | 0.65 | 0.81 | 38 | empty |
| 5 | 285 | 0.59 | 0.78 | 34 | empty |
Interfaces
3 interfaces between chains.
- C–B · 762 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 738 Ų buried · 8 hydrogen bonds · protein-protein
- C–A · 120 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7DJL · Structure of four truncated and mutated forms of quenching protein · the same entry in another collection · chain C against C, TM-score 1.00
- Q8VZ10 · AlphaFold monomer V2.0 prediction for protein suppressor of quenching 1, chloroplastic… · a predicted model of the same protein · chain B against A, TM-score 0.73
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 Q8VZ10
- Elsewhere: RCSB PDB 7DJL · PDBe 7DJL · UniProt Q8VZ10
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