Research workbench
Crystal structure of deskc-H188V in complex with ADP
Analyse Crystal structure of deskc-H188V in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EHH
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensor kinase (yocf protein)
- EC
- 2.7.13.3
- UniProt
- O34757
- Ligands
- ADP, CA
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor kinase (yocf protein) (EC 2.7.13.3) | protein | 192 | 58% helix, 17% strand | O34757 |
| B | Sensor kinase (yocf protein) (EC 2.7.13.3) | protein | 193 | 52% helix, 17% strand | O34757 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.57 | 0.89 | 16 | ADP |
| 2 | 92 | 0.53 | 0.84 | 20 | ADP |
| 3 | 53 | 0.29 | 0.75 | 14 | empty |
| 4 | 51 | 0.27 | 0.75 | 11 | empty |
| 5 | 57 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1650 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
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 O34757
- Elsewhere: RCSB PDB 3EHH · PDBe 3EHH · UniProt O34757
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