MolNFT v1 · #46976 · protein
Crystal structure of unknown conserved ybaa protein from shigella flexneri
2OKQ · Hypothetical protein ybaa: “Crystal structure of unknown conserved ybaa protein from shigella flexneri”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.65). MolNFT v1 #46976 on GenesisL1: 3D structure, binding…
- PDB
- 2OKQ
- Type
- protein
- Length
- 245 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein ybaa
- UniProt
- P0AAQ9
- Ligands
- NA
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein ybaa | protein | 127 | 37% helix, 31% strand | P0AAQ9 |
| B | Hypothetical protein ybaa | protein | 118 | 36% helix, 33% strand | P0AAQ9 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
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 | 342 | 0.65 | 0.80 | 37 | empty |
| 2 | 157 | 0.51 | 0.78 | 20 | empty |
| 3 | 153 | 0.48 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2231 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 2OKQ · Crystal structure of unknown conserved ybaA protein from Shigella flexneri · the same entry in another collection · chain A against A, TM-score 1.00
- P0AAQ9 · AlphaFold monomer V2.0 prediction for uncharacterized protein ybaa (P0AAQ9) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P0AAQ9
- Elsewhere: RCSB PDB 2OKQ · PDBe 2OKQ · UniProt P0AAQ9
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