MolNFT v1 · #129395 · protein
Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh) D182A variant in complex with mannosylglycerate
5OJ4: “Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh) D182A variant in complex…”. X-ray diffraction, 2 ligands (GLY, 2M8), 4 pockets (best druggability 0.83). MolNFT v1 #129395 on GenesisL1: 3D…
- PDB
- 5OJ4
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase
- UniProt
- K5BDL0
- Ligands
- GLY, 2M8
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hydrolase | protein | 445 | 51% helix, 6% strand | K5BDL0 |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, B
- 2M8 · (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 15 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.83 | 0.85 | 78 | GOL |
| 2 | 72 | 0.76 | 0.99 | 21 | 2M8 |
| 3 | 70 | 0.75 | 0.99 | 22 | 2M8 |
| 4 | 55 | 0.48 | 0.85 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 619 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5OJ4 · Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH)… · the same entry in another collection · chain B against B, TM-score 1.00
- K5BDL0 · AlphaFold monomer V2.0 prediction for glucosylglycerate hydrolase (K5BDL0) · a predicted model of the same protein · 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 K5BDL0
- Elsewhere: RCSB PDB 5OJ4 · PDBe 5OJ4 · UniProt K5BDL0
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