MolNFT v1 · #134501 · protein
X-ray structure of the C3-methyltransferase KIJD1 from actinomadura kijaniata in complex with tdp and sah
5T64 · Sugar 3-C-methyl transferase: “X-ray structure of the C3-methyltransferase KIJD1 from actinomadura kijaniata in complex with tdp and sah”. X-ray diffraction, 4 ligands (SAH, TMP, MG), 6 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5T64
- Type
- protein
- Length
- 803 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar 3-C-methyl transferase
- UniProt
- B3TMQ9
- Ligands
- SAH, TMP, MG, ZN
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar 3-C-methyl transferase | protein | 406 | 39% helix, 24% strand | B3TMQ9 |
| B | Sugar 3-C-methyl transferase | protein | 397 | 40% helix, 25% strand | B3TMQ9 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.83 | 0.87 | 60 | SAH, TMP |
| 2 | 829 | 0.81 | 0.83 | 103 | SAH, EDO, TMP |
| 3 | 76 | 0.46 | 0.82 | 18 | EDO |
| 4 | 100 | 0.46 | 0.80 | 19 | empty |
| 5 | 57 | 0.40 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 861 Ų buried · 6 hydrogen bonds · protein-protein
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 B3TMQ9
- Elsewhere: RCSB PDB 5T64 · PDBe 5T64 · UniProt B3TMQ9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.