MolNFT v1 · #116637 · protein
Thermobaculum terrenum O-glcnac transferase mutant - K341M
5DJS · Tetratricopeptide TPR_2 repeat protein: “Thermobaculum terrenum O-glcnac transferase mutant - K341M”. X-ray diffraction, 1 ligand (UDP), 20 pockets (best druggability 0.82). MolNFT v1 #116637 on GenesisL1: 3D structure, binding…
- PDB
- 5DJS
- Type
- protein
- Length
- 2,080 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetratricopeptide TPR_2 repeat protein
- UniProt
- D1CIY5
- Ligands
- UDP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tetratricopeptide TPR_2 repeat protein | protein | 520 | 54% helix, 11% strand | D1CIY5 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.82 | 0.83 | 80 | UDP |
| 2 | 1193 | 0.80 | 0.81 | 86 | UDP |
| 3 | 1142 | 0.80 | 0.81 | 85 | UDP |
| 4 | 1060 | 0.80 | 0.81 | 77 | UDP |
| 5 | 461 | 0.67 | 0.79 | 53 | empty |
Interfaces
5 interfaces between chains.
- B–D · 946 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 945 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 931 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 232 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DJS · Thermobaculum terrenum O-GlcNAc transferase mutant - K341M · 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 D1CIY5
- Elsewhere: RCSB PDB 5DJS · PDBe 5DJS · UniProt D1CIY5
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