MolNFT v1 · #60507 · protein
Crystal structure of periplasmic binding PROTEIN/LACI transcriptional regulator from alkaliphilus metalliredigens qymf complexed with D- xylulofuranose
3CTP: “Crystal structure of periplasmic binding PROTEIN/LACI transcriptional regulator from alkaliphilus…”. X-ray diffraction, 2 ligands (XLF, NA), 7 pockets (best druggability 0.54). MolNFT v1 #60507 on GenesisL1: 3D structure, binding…
- PDB
- 3CTP
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding PROTEIN/LACI transcriptional regulator
- UniProt
- A6TKU5
- Ligands
- XLF, NA
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 266 | 40% helix, 20% strand | A6TKU5 |
Ligands and binding sites
- XLF · beta-D-xylulofuranose · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.54 | 0.76 | 46 | empty |
| 2 | 115 | 0.48 | 0.79 | 20 | empty |
| 3 | 172 | 0.48 | 0.76 | 27 | empty |
| 4 | 102 | 0.45 | 0.79 | 18 | empty |
| 5 | 91 | 0.33 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1748 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3CTP · Crystal structure of periplasmic binding protein/LacI transcriptional regulator from… · 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 A6TKU5
- Elsewhere: RCSB PDB 3CTP · PDBe 3CTP · UniProt A6TKU5
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