MolNFT v1 · #127193 · protein
Crystal structure of phosphoribosylpyrophosphate synthetase from mycobacterium smegmatis
5MP7 · Ribose-phosphate pyrophosphokinase: “Crystal structure of phosphoribosylpyrophosphate synthetase from mycobacterium smegmatis”. X-ray diffraction, 5 pockets (best druggability 0.72). MolNFT v1 #127193 on GenesisL1: 3D structure…
- PDB
- 5MP7
- Type
- protein
- Length
- 894 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- A0R3C8
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 298 | 36% helix, 27% strand | A0R3C8 |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.72 | 0.77 | 100 | ACT |
| 2 | 264 | 0.59 | 0.79 | 44 | ACT |
| 3 | 254 | 0.59 | 0.79 | 42 | ACT |
| 4 | 80 | 0.38 | 0.77 | 19 | empty |
| 5 | 79 | 0.34 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2112 Ų buried · 21 hydrogen bonds · protein-protein
- C–B · 388 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MP7 · Crystal structure of phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis · 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 A0R3C8
- Elsewhere: RCSB PDB 5MP7 · PDBe 5MP7 · UniProt A0R3C8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.