Research workbench
Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon thermococcus kodakaraensis, in complex with glucose and additives
Analyse Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N98
- Type
- protein
- Length
- 550 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase, GH57 family
- EC
- 2.4.1.18
- UniProt
- Q5JDJ7
- Ligands
- BGC
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase, GH57 family (EC 2.4.1.18) | protein | 550 | 51% helix, 12% strand | Q5JDJ7 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.75 | 0.82 | 52 | BGC, GOL |
| 2 | 178 | 0.53 | 0.78 | 22 | DIO |
| 3 | 140 | 0.53 | 0.81 | 17 | empty |
| 4 | 119 | 0.42 | 0.76 | 23 | empty |
| 5 | 110 | 0.39 | 0.75 | 26 | empty |
Compared structures
- 3N98 · Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JDJ7 · AlphaFold monomer V2.0 prediction for 1,4-alpha-glucan branching enzyme TK1436 (Q5JDJ7) · 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 Q5JDJ7
- Elsewhere: RCSB PDB 3N98 · PDBe 3N98 · UniProt Q5JDJ7
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