Research workbench
Non-square conformations of ktra E125Q mutant rings with bound ADP
Analyse Non-square conformations of ktra E125Q mutant rings with bound ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S5O
- Type
- protein
- Length
- 1,556 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ktr system potassium uptake protein a
- UniProt
- O32080
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ktr system potassium uptake protein a | protein | 215 | 36% helix, 27% strand | O32080 |
| G, H | Ktr system potassium uptake protein a | protein | 133 | 47% helix, 18% strand | O32080 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 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
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.58 | 0.75 | 31 | empty |
| 2 | 334 | 0.57 | 0.76 | 32 | empty |
| 3 | 127 | 0.56 | 0.83 | 19 | empty |
| 4 | 184 | 0.54 | 0.79 | 21 | empty |
| 5 | 111 | 0.54 | 0.83 | 16 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2455 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2441 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2368 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1656 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 575 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6S5O · Non-square conformations of KtrA E125Q mutant rings with bound ADP · the same entry in another collection · chain G against G, TM-score 1.00
- O32080 · AlphaFold monomer V2.0 prediction for ktr system potassium uptake protein a (O32080) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O32080
- Elsewhere: RCSB PDB 6S5O · PDBe 6S5O · UniProt O32080
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