MolNFT v1 · #129361 · protein
Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh) - semet derivative
5OHZ: “Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh) - semet derivative”. X-ray diffraction, 1 ligand (SER), 12 pockets (best druggability 0.85). MolNFT v1 #129361 on GenesisL1: 3D structure, binding…
- PDB
- 5OHZ
- Type
- protein
- Length
- 1,771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase
- UniProt
- K5BDL0
- Ligands
- SER
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase | protein | 443 | 51% helix, 6% strand | K5BDL0 |
| B, D | Hydrolase | protein | 442 | 51% helix, 6% strand | K5BDL0 |
| C | Hydrolase | protein | 444 | 51% helix, 6% strand | K5BDL0 |
Ligands and binding sites
- SER · Serine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 16 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.85 | 0.87 | 103 | GOL |
| 2 | 1166 | 0.84 | 0.85 | 103 | GOL |
| 3 | 72 | 0.75 | 0.99 | 21 | GOL, SER |
| 4 | 66 | 0.74 | 0.98 | 21 | GOL, SER |
| 5 | 69 | 0.73 | 0.98 | 23 | GOL, SER |
Interfaces
6 interfaces between chains.
- C–D · 1116 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1111 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 603 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 601 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 173 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered, nonstandard).
Compared structures
- 5OHZ · Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH)… · the same entry in another collection · chain D against D, 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 5OHZ · PDBe 5OHZ · UniProt K5BDL0
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