MolNFT v1 · #109190 · protein
Crystal structure of GH63 mannosylglycerate hydrolase from thermus thermophilus HB8 in complex with tris
4WVA · Uncharacterized protein: “Crystal structure of GH63 mannosylglycerate hydrolase from thermus thermophilus HB8 in complex with tris”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.72). MolNFT v1 #109190 on…
- PDB
- 4WVA
- Type
- protein
- Length
- 827 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q5SJN0
- Ligands
- CL
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 413 | 53% helix, 8% strand | Q5SJN0 |
| B | Uncharacterized protein | protein | 414 | 53% helix, 8% strand | Q5SJN0 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.72 | 0.99 | 19 | TRS |
| 2 | 634 | 0.68 | 0.76 | 62 | MPD |
| 3 | 381 | 0.67 | 0.80 | 39 | TRS |
| 4 | 80 | 0.43 | 0.79 | 16 | MPD |
| 5 | 84 | 0.42 | 0.79 | 17 | MPD |
Interfaces
1 interface between chains.
- A–B · 108 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4WVA · 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 4WVA · PDBe 4WVA · UniProt Q5SJN0
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