MolNFT v1 · #11946 · protein
Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis
1K1X: “Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.73). MolNFT v1 #11946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K1X
- 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
- CA
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 636 | 33% helix, 31% strand | O32462 |
| B | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 636 | 35% helix, 30% strand | O32462 |
Ligands and binding sites
- 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.73 | 0.81 | 48 | empty |
| 2 | 772 | 0.71 | 0.77 | 61 | TRS |
| 3 | 611 | 0.69 | 0.77 | 58 | empty |
| 4 | 512 | 0.68 | 0.79 | 50 | empty |
| 5 | 244 | 0.58 | 0.79 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2391 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1K1X · Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis · 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 1K1X · PDBe 1K1X · UniProt O32462
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