MolNFT v1 · #129564 · protein
Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh) E419A variant in complex with glucosylglycolate
5OO2 · Uncharacterized protein: “Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh) E419A variant in complex…”. X-ray diffraction, 2 ligands (9YW, SER), 5 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5OO2
- 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
- 9YW, SER
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 445 | 51% helix, 7% strand | K5BDL0 |
Ligands and binding sites
- 9YW · (alpha-D-glucopyranosyloxy)acetic acid · ligand · 2 copies · chains A, B
- SER · Serine · ligand · chains A
- GOL · Glycerol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.84 | 0.85 | 93 | empty |
| 2 | 112 | 0.79 | 0.97 | 33 | 9YW |
| 3 | 81 | 0.77 | 0.99 | 23 | GOL, 9YW, SER |
| 4 | 52 | 0.34 | 0.79 | 14 | empty |
| 5 | 50 | 0.33 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 630 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5OO2 · Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH)… · the same entry in another collection · chain A against A, 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 5OO2 · PDBe 5OO2 · UniProt K5BDL0
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