MolNFT v1 · #11947 · protein
Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with acarbose
1K1Y: “Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with acarbose”. X-ray diffraction, 3 ligands (AC1, GLC, CA), 8 pockets (best druggability 0.74). MolNFT v1 #11947 on GenesisL1: 3D structure, binding…
- PDB
- 1K1Y
- Type
- protein
- Length
- 1,272 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-alpha-glucanotransferase
- EC
- 2.4.1.25
- UniProt
- O32462
- Ligands
- AC1, GLC, CA
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 636 | 34% helix, 31% strand | O32462 |
| B | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 636 | 35% helix, 30% strand | O32462 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.74 | 0.78 | 74 | GLC, AC1 |
| 2 | 830 | 0.73 | 0.78 | 70 | GLC, TRS |
| 3 | 51 | 0.70 | 0.98 | 29 | empty |
| 4 | 588 | 0.69 | 0.78 | 55 | empty |
| 5 | 501 | 0.68 | 0.79 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 2391 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1K1Y · Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- O32462 · AlphaFold monomer V2.0 prediction for 4-alpha-glucanotransferase (O32462) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O32462
- Elsewhere: RCSB PDB 1K1Y · PDBe 1K1Y · UniProt O32462
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