MolNFT v1 · #129420 · protein
Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh) E419A variant in complex with mannosylglycerate
5OJV · Uncharacterized protein: “Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh) E419A variant in complex…”. X-ray diffraction, 2 ligands (2M8, SER), 3 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5OJV
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- K5BDL0
- Ligands
- 2M8, SER
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 445 | 50% helix, 6% strand | K5BDL0 |
Ligands and binding sites
- 2M8 · (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid · ligand · 2 copies · chains A, B
- SER · Serine · ligand · chains A
- GOL · Glycerol · additive · 9 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.84 | 0.85 | 88 | empty |
| 2 | 84 | 0.78 | 0.99 | 24 | GOL, 2M8, SER |
| 3 | 78 | 0.76 | 0.98 | 26 | 2M8 |
Interfaces
1 interface between chains.
- A–B · 622 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5OJV · 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 5OJV · PDBe 5OJV · UniProt K5BDL0
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