MolNFT v1 · #141762 · protein
Crystal structure of type-II log from streptomyces coelicolor A3
5ZI9 · Cytokinin riboside 5'-monophosphate phosphoribohydrolase: “Crystal structure of type-II log from streptomyces coelicolor A3”. X-ray diffraction, 8 pockets (best druggability 0.76). MolNFT v1 #141762 on GenesisL1: 3D structure…
- PDB
- 5ZI9
- Type
- protein
- Length
- 898 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
- Q9FBL8
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 209 | 50% helix, 14% strand | Q9FBL8 |
| B, D | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 240 | 48% helix, 17% strand | Q9FBL8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.76 | 0.88 | 35 | EDO, FLC |
| 2 | 282 | 0.75 | 0.88 | 38 | EDO, FLC |
| 3 | 357 | 0.73 | 0.84 | 37 | EDO, FLC |
| 4 | 351 | 0.72 | 0.84 | 39 | EDO, FLC |
| 5 | 261 | 0.55 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2407 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2396 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5ZI9 · Crystal structure of type-II LOG from Streptomyces coelicolor A3 · 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 Q9FBL8
- Elsewhere: RCSB PDB 5ZI9 · PDBe 5ZI9 · UniProt Q9FBL8
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