MolNFT v1 · #39204 · protein
Rectangular-shaped octameric ring structure of an rck domain with NADH bound
2HMS · Yuaa protein: “Rectangular-shaped octameric ring structure of an rck domain with NADH bound”. X-ray diffraction, 1 ligand (NAI), 4 pockets (best druggability 0.42). MolNFT v1 #39204 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2HMS
- Type
- protein
- Length
- 544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yuaa protein
- UniProt
- O32080
- Ligands
- NAI
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Yuaa protein | protein | 138 | 49% helix, 20% strand | O32080 |
| B, D | Yuaa protein | protein | 134 | 47% helix, 19% strand | O32080 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.42 | 0.79 | 26 | NAI |
| 2 | 92 | 0.38 | 0.76 | 25 | NAI |
| 3 | 75 | 0.35 | 0.76 | 23 | NAI |
| 4 | 75 | 0.33 | 0.75 | 23 | NAI |
Interfaces
3 interfaces between chains.
- C–D · 1736 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1730 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 837 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2HMS · Rectangular-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 0.95
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 O32080
- Elsewhere: RCSB PDB 2HMS · PDBe 2HMS · UniProt O32080
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