MolNFT v1 · #12289 · protein
Endopolygalacturonase I from stereum purpureum complexed with a galacturonate at 1.00 a resolution.
1KCC: “Endopolygalacturonase I from stereum purpureum complexed with a galacturonate at 1.00 a resolution.”. X-ray diffraction, 4 ligands (GTR, NAG, NA), 1 pocket (best druggability 0.26). MolNFT v1 #12289 on GenesisL1: 3D structure…
- PDB
- 1KCC
- Type
- protein
- Length
- 333 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endopolygalacturonase
- EC
- 3.2.1.15
- UniProt
- P79074
- Ligands
- GTR, NAG, NA, CL
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endopolygalacturonase (EC 3.2.1.15) | protein | 333 | 4% helix, 52% strand | P79074 |
Ligands and binding sites
- GTR · beta-D-galactopyranuronic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.26 | 0.72 | 22 | GTR |
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1KCC · Endopolygalacturonase I from Stereum purpureum complexed with a galacturonate at 1.00 A… · 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 P79074
- Elsewhere: RCSB PDB 1KCC · PDBe 1KCC · UniProt P79074
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