Research workbench
X-ray structure of the endo-beta-1,4-mannanase from thermotoga petrophila
Analyse X-ray structure of the endo-beta-1,4-mannanase from thermotoga petrophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TN6
- Type
- protein
- Length
- 465 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannan endo-1,4-beta-mannosidase. glycosyl hydrolase family 5
- EC
- 3.2.1.78
- UniProt
- A5IMX7
- Ligands
- NA, CO3, CL
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannan endo-1,4-beta-mannosidase. glycosyl hydrolase family 5 (EC 3.2.1.78) | protein | 465 | 33% helix, 26% strand | A5IMX7 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CO3 · Carbonate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.51 | 0.83 | 14 | ACT |
| 2 | 159 | 0.46 | 0.76 | 26 | CO3, TRS |
| 3 | 75 | 0.34 | 0.75 | 16 | empty |
Compared structures
- 6TN6 · X-ray structure of the endo-beta-1,4-mannanase from Thermotoga petrophila · 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 A5IMX7
- Elsewhere: RCSB PDB 6TN6 · PDBe 6TN6 · UniProt A5IMX7
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