Research workbench
Crystal structure of GH63 mannosylglycerate hydrolase from thermus thermophilus HB8 in complex with glucose
Analyse Crystal structure of GH63 mannosylglycerate hydrolase from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WVB
- Type
- protein
- Length
- 811 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q5SJN0
- Ligands
- GLC, CL
- Pockets
- 6 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 394 | 53% helix, 10% strand | Q5SJN0 |
| B | Uncharacterized protein | protein | 417 | 51% helix, 10% strand | Q5SJN0 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.90 | 0.92 | 114 | MPD |
| 2 | 248 | 0.69 | 0.84 | 37 | empty |
| 3 | 77 | 0.52 | 0.84 | 18 | GLC |
| 4 | 97 | 0.46 | 0.80 | 20 | empty |
| 5 | 86 | 0.41 | 0.78 | 16 | MPD |
Interfaces
1 interface between chains.
- A–B · 1610 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4WVB · Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in… · 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 Q5SJN0
- Elsewhere: RCSB PDB 4WVB · PDBe 4WVB · UniProt Q5SJN0
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