MolNFT v1 · #112476 · protein
Crystal structure of a five-domain GH115 alpha-glucuronidase from the marine bacterium saccharophagus degradans 2-40T
4ZMH · Uncharacterized protein: “Crystal structure of a five-domain GH115 alpha-glucuronidase from the marine bacterium saccharophagus…”. X-ray diffraction, 2 ligands (NA, PO4), 20 pockets (best druggability 0.80). MolNFT v1 #112476 on…
- PDB
- 4ZMH
- Type
- protein
- Length
- 1,866 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q21JW4
- Ligands
- NA, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 935 | 32% helix, 24% strand | Q21JW4 |
| B | Uncharacterized protein | protein | 931 | 33% helix, 24% strand | Q21JW4 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.80 | 0.82 | 94 | empty |
| 2 | 85 | 0.76 | 0.98 | 33 | empty |
| 3 | 86 | 0.75 | 0.98 | 33 | empty |
| 4 | 476 | 0.69 | 0.80 | 54 | empty |
| 5 | 430 | 0.68 | 0.80 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 1481 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 modified (engineered).
Compared structures
- 4ZMH · Crystal structure of a five-domain GH115 alpha-Glucuronidase from the Marine Bacterium… · 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 Q21JW4
- Elsewhere: RCSB PDB 4ZMH · PDBe 4ZMH · UniProt Q21JW4
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