Research workbench
Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with 3-isobutyl-1-methylxanthine (ibmx) and PDE6 gamma-subunit inhibitory peptide 70-87.
Analyse Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JWR
- Type
- protein
- Length
- 685 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific 3',5'-cyclic phosphodiesterase catalytic domain, cone cgmp-specific…
- EC
- 3.1.4.35, 3.1.4.17
- UniProt
- O76074, P51160, P18545
- Ligands
- IBM, ZN, MG
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase catalytic domain, cone cgmp-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera (EC 3.1.4.35) | protein | 323 | 71% helix, 0% strand | O76074, P51160 |
| B | Cgmp-specific 3',5'-cyclic phosphodiesterase catalytic domain, cone cgmp-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera (EC 3.1.4.35) | protein | 328 | 71% helix, 0% strand | O76074, P51160 |
| C, D | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit gamma (EC 3.1.4.17) | protein | 17 | 35% helix, 0% strand | P18545 |
Ligands and binding sites
- IBM · 3-isobutyl-1-methylxanthine · ligand · 5 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.86 | 0.94 | 52 | MG, IBM |
| 2 | 410 | 0.86 | 0.94 | 51 | MG, IBM |
| 3 | 822 | 0.76 | 0.80 | 81 | empty |
| 4 | 61 | 0.50 | 0.86 | 22 | empty |
| 5 | 69 | 0.42 | 0.81 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 669 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 615 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 606 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3JWR · Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- O76074 · AlphaFold monomer V2.0 prediction for cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P51160 · AlphaFold monomer V2.0 prediction for cone cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P18545 · 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 0.32
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 O76074
- Every structure of UniProt P51160
- Every structure of UniProt P18545
- Elsewhere: RCSB PDB 3JWR · PDBe 3JWR · UniProt O76074 · UniProt P51160 · UniProt P18545
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