Research workbench
Diamond-shaped octameric ring structure of an rck domain with NADH bound
Analyse Diamond-shaped octameric ring structure of an rck domain with NADH bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HMT
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yuaa protein
- UniProt
- O32080
- Ligands
- NAI
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yuaa protein | protein | 139 | 47% helix, 17% strand | O32080 |
| B | Yuaa protein | protein | 135 | 49% helix, 18% strand | O32080 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.38 | 0.77 | 24 | NAI |
| 2 | 81 | 0.36 | 0.76 | 26 | NAI |
Interfaces
1 interface between chains.
- A–B · 1702 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2HMT · Diamond-shaped octameric ring structure of an RCK domain with NADH bound · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.94
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 2HMT · PDBe 2HMT · UniProt O32080
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