MolNFT v1 · #141562 · protein
Crystal structure of type-I log from corynebacterium glutamicum in complex with AMP
5ZBL · Cytokinin riboside 5'-monophosphate phosphoribohydrolase: “Crystal structure of type-I log from corynebacterium glutamicum in complex with AMP”. X-ray diffraction, 3 ligands (AMP, SO4, PO4), 6 pockets (best druggability 0.79).…
- PDB
- 5ZBL
- Type
- protein
- Length
- 733 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
- AMP, SO4, PO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 189 | 46% helix, 17% strand | Q8NN34 |
| B | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 187 | 48% helix, 17% strand | Q8NN34 |
| C | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 176 | 46% helix, 16% strand | Q8NN34 |
| D | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 181 | 49% helix, 18% strand | Q8NN34 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.79 | 0.81 | 108 | GOL, PO4, SO4 |
| 2 | 910 | 0.77 | 0.80 | 100 | AMP, GOL |
| 3 | 51 | 0.55 | 0.89 | 22 | empty |
| 4 | 116 | 0.38 | 0.74 | 20 | empty |
| 5 | 65 | 0.34 | 0.76 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1561 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1522 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 719 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5ZBL · Crystal structure of type-I LOG from Corynebacterium glutamicum in complex with AMP · 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 5ZBL · PDBe 5ZBL · UniProt Q8NN34
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