MolNFT v1 · #57044 · protein
Crystal structure of CYCLO/MALTODEXTRIN-binding protein complexed with gamma-cyclodextrin
2ZYK · Solute-binding protein: “Crystal structure of CYCLO/MALTODEXTRIN-binding protein complexed with gamma-cyclodextrin”. X-ray diffraction, 1 ligand (GLC), 18 pockets (best druggability 0.80). MolNFT v1 #57044 on GenesisL1: 3D…
- PDB
- 2ZYK
- Type
- protein
- Length
- 1,524 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Solute-binding protein
- UniProt
- Q9AJF5
- Ligands
- GLC
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Solute-binding protein | protein | 381 | 46% helix, 20% strand | Q9AJF5 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 32 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.80 | 0.87 | 74 | empty |
| 2 | 370 | 0.77 | 0.87 | 45 | empty |
| 3 | 618 | 0.68 | 0.77 | 52 | GLC |
| 4 | 718 | 0.67 | 0.75 | 60 | empty |
| 5 | 420 | 0.66 | 0.79 | 57 | empty |
Interfaces
5 interfaces between chains.
- C–D · 614 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 592 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 520 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 457 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 320 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2ZYK · Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin · 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 Q9AJF5
- Elsewhere: RCSB PDB 2ZYK · PDBe 2ZYK · UniProt Q9AJF5
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