MolNFT v1 · #74036 · protein
Crystal structure of yaeb-like protein from rhodopseudomonas palustris
3OKX · Yaeb-like protein RPA0152: “Crystal structure of yaeb-like protein from rhodopseudomonas palustris”. X-ray diffraction, 1 ligand (SAM), 3 pockets (best druggability 0.72). MolNFT v1 #74036 on GenesisL1: 3D structure, binding sites…
- PDB
- 3OKX
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yaeb-like protein RPA0152
- UniProt
- Q6NDF6
- Ligands
- SAM
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yaeb-like protein RPA0152 | protein | 156 | 13% helix, 33% strand | Q6NDF6 |
| B | Yaeb-like protein RPA0152 | protein | 149 | 11% helix, 36% strand | Q6NDF6 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.72 | 0.83 | 43 | SAM |
| 2 | 275 | 0.64 | 0.81 | 36 | SAM |
| 3 | 60 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3159 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 3OKX · Crystal structure of YaeB-like protein from Rhodopseudomonas palustris · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NDF6 · AlphaFold monomer V2.0 prediction for S-adenosyl-L-methionine-binding protein RPA0152… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6NDF6
- Elsewhere: RCSB PDB 3OKX · PDBe 3OKX · UniProt Q6NDF6
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