MolNFT v1 · #139870 · protein
Xylfii molecule
5XSS · Periplasmic binding PROTEIN/LACI transcriptional regulator: “Xylfii molecule”. X-ray diffraction, 1 ligand (XYP), 13 pockets (best druggability 0.73). MolNFT v1 #139870 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XSS
- Type
- protein
- Length
- 1,087 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding PROTEIN/LACI transcriptional regulator
- UniProt
- A6LW07
- Ligands
- XYP
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 271 | 45% helix, 19% strand | A6LW07 |
| A | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 274 | 45% helix, 19% strand | A6LW07 |
| B | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 272 | 45% helix, 18% strand | A6LW07 |
| C | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 270 | 45% helix, 19% strand | A6LW07 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains X, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.73 | 0.82 | 56 | empty |
| 2 | 393 | 0.55 | 0.73 | 48 | empty |
| 3 | 120 | 0.47 | 0.79 | 29 | empty |
| 4 | 173 | 0.46 | 0.76 | 29 | empty |
| 5 | 174 | 0.46 | 0.75 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 643 Ų buried · 9 hydrogen bonds · protein-protein
- X–C · 637 Ų buried · 9 hydrogen bonds · protein-protein
- X–B · 486 Ų buried · 13 hydrogen bonds · protein-protein
- X–A · 188 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 99 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5XSS · XylFII molecule · the same entry in another collection · chain X against X, 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 A6LW07
- Elsewhere: RCSB PDB 5XSS · PDBe 5XSS · UniProt A6LW07
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