Research workbench
Crystal structure of a domain of unknown function (DUF1537) from Ralstonia eutropha H16 (H16_A1561), Target EFI-511666, complex with ADP.
Analyse Crystal structure of a domain of unknown function (DUF1537) from Ralstonia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DMH
- Type
- protein
- Length
- 836 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)
- Molecule
- Uncharacterized protein conserved in bacteria
- UniProt
- Q0KBC8
- Ligands
- ADP
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein conserved in bacteria | protein | 420 | 41% helix, 21% strand | Q0KBC8 |
| B | Uncharacterized protein conserved in bacteria | protein | 416 | 42% helix, 21% strand | Q0KBC8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
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 | 298 | 0.76 | 0.88 | 47 | ADP |
| 2 | 506 | 0.62 | 0.75 | 64 | empty |
| 3 | 201 | 0.58 | 0.80 | 39 | empty |
| 4 | 160 | 0.57 | 0.82 | 22 | empty |
| 5 | 100 | 0.36 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 378 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5DMH · Crystal structure of a domain of unknown function (DUF1537) from ralstonia eutropha H16… · the same entry in another collection · chain A against A, TM-score 1.00
- Q0KBC8 · AlphaFold monomer V2.0 prediction for 3-oxo-tetronate kinase (Q0KBC8) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q0KBC8
- Elsewhere: RCSB PDB 5DMH · PDBe 5DMH · UniProt Q0KBC8
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