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Crystal structure of GH63 mannosylglycerate hydrolase from thermus thermophilus HB8 in complex with tris and D-glycerate
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
- 4WVC
- Type
- protein
- Length
- 822 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q5SJN0
- Ligands
- DGY, CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 413 | 54% helix, 7% strand | Q5SJN0 |
| B | Uncharacterized protein | protein | 409 | 52% helix, 7% strand | Q5SJN0 |
Ligands and binding sites
- DGY · (2R)-2,3-dihydroxypropanoic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.82 | 0.83 | 97 | empty |
| 2 | 61 | 0.74 | 0.99 | 20 | TRS, DGY |
| 3 | 52 | 0.71 | 0.98 | 19 | TRS, DGY |
| 4 | 99 | 0.53 | 0.83 | 25 | empty |
| 5 | 80 | 0.41 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 588 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4WVC · 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 4WVC · PDBe 4WVC · UniProt Q5SJN0
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