Research workbench
Crystal structure of log from corynebacterium glutamicum
Analyse Crystal structure of log from corynebacterium glutamicum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ITS
- Type
- protein
- Length
- 762 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytokinin riboside 5'-monophosphate phosphoribohydrolase
- EC
- 3.2.2.-
- UniProt
- Q8NN34
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 183 | 48% helix, 17% strand | Q8NN34 |
| B | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 195 | 46% helix, 16% strand | Q8NN34 |
| C | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 188 | 46% helix, 18% strand | Q8NN34 |
| D | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 196 | 45% helix, 16% strand | Q8NN34 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, D, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.80 | 0.81 | 120 | PO4, GOL |
| 2 | 102 | 0.76 | 0.96 | 31 | PO4, GOL |
| 3 | 89 | 0.72 | 0.95 | 28 | empty |
| 4 | 243 | 0.69 | 0.85 | 35 | empty |
| 5 | 308 | 0.66 | 0.81 | 42 | GOL |
Interfaces
5 interfaces between chains.
- C–D · 1653 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1614 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1038 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 333 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 261 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ITS · Crystal structure of LOG from Corynebacterium glutamicum · 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 Q8NN34
- Elsewhere: RCSB PDB 5ITS · PDBe 5ITS · UniProt Q8NN34
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.