MolNFT v1 · #153474 · protein
Crystal structure of pullulanase from paenibacillus barengoltzii complex with maltohexaose and alpha-cyclodextrin
6JFJ · Pulullanase: “Crystal structure of pullulanase from paenibacillus barengoltzii complex with maltohexaose and…”. X-ray diffraction, 4 ligands (TAM, GLC, CA), 6 pockets (best druggability 0.56). MolNFT v1 #153474 on GenesisL1: 3D…
- PDB
- 6JFJ
- Type
- protein
- Length
- 646 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulullanase
- EC
- 3.2.1.41
- UniProt
- A0A0C5GWS2
- Ligands
- TAM, GLC, CA, CL
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pulullanase (EC 3.2.1.41) | protein | 646 | 32% helix, 23% strand | A0A0C5GWS2 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 11 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 8 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- IMD · Imidazole · additive · 4 copies · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.56 | 0.77 | 31 | GLC |
| 2 | 182 | 0.53 | 0.79 | 29 | empty |
| 3 | 70 | 0.38 | 0.78 | 19 | PEG, CL |
| 4 | 72 | 0.36 | 0.77 | 17 | empty |
| 5 | 55 | 0.34 | 0.78 | 20 | CA |
Compared structures
- 6JFJ · Crystal structure of Pullulanase from Paenibacillus barengoltzii complex with… · 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 A0A0C5GWS2
- Elsewhere: RCSB PDB 6JFJ · PDBe 6JFJ · UniProt A0A0C5GWS2
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