MolNFT v1 · #166688 · protein
Crystal structure of unknown function protein yfdx from shigella flexneri
6UXT · Yfdx protein: “Crystal structure of unknown function protein yfdx from shigella flexneri”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #166688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6UXT
- Type
- protein
- Length
- 1,306 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfdx protein
- UniProt
- A0A2Y2P124
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G, H | Yfdx protein | protein | 163 | 56% helix, 17% strand | A0A2Y2P124 |
| C, D | Yfdx protein | protein | 164 | 56% helix, 18% strand | A0A2Y2P124 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 2 copies · chains B, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.78 | 0.80 | 102 | empty |
| 2 | 555 | 0.70 | 0.79 | 58 | empty |
| 3 | 345 | 0.66 | 0.80 | 28 | PGE, EPE |
| 4 | 445 | 0.65 | 0.78 | 56 | empty |
| 5 | 248 | 0.63 | 0.81 | 33 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1678 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1647 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1627 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 1261 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6UXT · Crystal structure of unknown function protein yfdX from Shigella flexneri · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A2Y2P124
- Elsewhere: RCSB PDB 6UXT · PDBe 6UXT · UniProt A0A2Y2P124
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