MolNFT v1 · #121736 · protein
Crystal structure of rimk domain protein ATP-grasp from sphaerobacter thermophilus dsm 20745
5I47: “Crystal structure of rimk domain protein ATP-grasp from sphaerobacter thermophilus dsm 20745”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #121736 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I47
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rimk domain protein ATP-grasp
- UniProt
- D1C6B4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rimk domain protein ATP-grasp | protein | 258 | 37% helix, 27% strand | D1C6B4 |
| B | Rimk domain protein ATP-grasp | protein | 264 | 37% helix, 27% strand | D1C6B4 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.76 | 0.79 | 110 | empty |
| 2 | 387 | 0.64 | 0.79 | 50 | empty |
| 3 | 285 | 0.61 | 0.79 | 44 | empty |
| 4 | 62 | 0.40 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1307 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 5I47 · Crystal structure of RimK domain protein ATP-grasp from Sphaerobacter thermophilus DSM… · 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 D1C6B4
- Elsewhere: RCSB PDB 5I47 · PDBe 5I47 · UniProt D1C6B4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.