MolNFT v1 · #9917 · protein
Crystal structure of polygalacturonase from aspergillus aculeatus at PH4.5
1IB4: “Crystal structure of polygalacturonase from aspergillus aculeatus at PH4.5”. X-ray diffraction, 3 ligands (MAN, NAG, CD), 3 pockets (best druggability 0.85). MolNFT v1 #9917 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1IB4
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polygalacturonase
- EC
- 3.2.1.15
- Ligands
- MAN, NAG, CD
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polygalacturonase (EC 3.2.1.15) | protein | 339 | 6% helix, 52% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 22 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CD · Cadmium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.85 | 0.87 | 122 | empty |
| 2 | 81 | 0.33 | 0.75 | 23 | empty |
| 3 | 72 | 0.30 | 0.74 | 24 | CD |
Interfaces
1 interface between chains.
- A–B · 1201 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 8 disulfide (O-glycosylation, disulfide, N-glycosylation).
Compared structures
- 1IB4 · Crystal Structure of Polygalacturonase from Aspergillus Aculeatus at Ph4.5 · 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
- Elsewhere: RCSB PDB 1IB4 · PDBe 1IB4
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