MolNFT v2 · #222059 · protein
Cryo-EM structure of bovine phosphodiesterase 6
8UFI · Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit…: “Cryo-EM structure of bovine phosphodiesterase 6”. Electron microscopy at 3.1, 3 ligands (PCG, ZN, MG), 20 pockets (best druggability 0.83). MolNFT v2 #222059 on GenesisL1…
- PDB
- 8UFI
- Type
- protein
- Length
- 1,734 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Bos taurus
- Molecule
- Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha; Rod cGMP-specific…
- EC
- 3.1.4.35
- UniProt
- P11541, P23439, P04972
- Ligands
- PCG, ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.1 · 4 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (EC 3.1.4.35) | protein | 816 | 54% helix, 10% strand | P11541 |
| B | Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta (EC 3.1.4.35) | protein | 821 | 54% helix, 11% strand | P23439 |
| C | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (EC 3.1.4.35) | protein | 48 | 17% helix, 4% strand | P04972 |
| D | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (EC 3.1.4.35) | protein | 49 | 18% helix, 2% strand | P04972 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.83 | 0.91 | 49 | MG |
| 2 | 383 | 0.81 | 0.90 | 50 | MG |
| 3 | 128 | 0.78 | 0.95 | 24 | PCG |
| 4 | 162 | 0.76 | 0.92 | 32 | PCG |
| 5 | 209 | 0.71 | 0.87 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6765 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 1898 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1883 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 656 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 589 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- P04972 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain C against A, TM-score 0.24
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 P11541
- Every structure of UniProt P23439
- Every structure of UniProt P04972
- Elsewhere: RCSB PDB 8UFI · PDBe 8UFI · UniProt P11541 · UniProt P23439 · UniProt P04972
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