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Domain organization and conformational plasticity of the G protein effector, PDE6
Analyse Domain organization and conformational plasticity of the G protein effector… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JAB
- Type
- protein
- Length
- 2,224 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gafa domain of cone phosphodiesterase 6C; Gafb domain of phosphodiesterase 2A…
- UniProt
- P04972
- Ligands
- IBM
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M | Gafa domain of cone phosphodiesterase 6C | protein | 171 | 40% helix, 28% strand | — |
| B, N | Gafb domain of phosphodiesterase 2A | protein | 161 | 48% helix, 18% strand | — |
| C, O | Phosphodiesterase 5/6 chimera catalytic domain | protein | 328 | 70% helix, 0% strand | — |
| D, P | Phosphodiesterase 6 gamma subunit inhibitory peptide | protein | 17 | 35% helix, 0% strand | P04972 |
| L, R | IGG1-kappa 2E8 light chain | protein | 214 | 5% helix, 49% strand | — |
| H, Q | IGG1-kappa 2E8 heavy chain | protein | 221 | 8% helix, 52% strand | — |
Ligands and binding sites
- IBM · 3-isobutyl-1-methylxanthine · ligand · 4 copies · chains C, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.86 | 0.94 | 52 | IBM |
| 2 | 408 | 0.86 | 0.94 | 49 | IBM |
| 3 | 145 | 0.77 | 0.94 | 25 | empty |
| 4 | 130 | 0.76 | 0.94 | 22 | empty |
| 5 | 362 | 0.63 | 0.78 | 59 | empty |
Interfaces
17 interfaces between chains.
- L–H · 1907 Ų buried · 17 hydrogen bonds · protein-protein
- R–Q · 1897 Ų buried · 17 hydrogen bonds · protein-protein
- A–M · 1073 Ų buried · 57 hydrogen bonds · protein-protein
- B–N · 898 Ų buried · 22 hydrogen bonds · protein-protein
- C–O · 815 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3JAB · Domain organization and conformational plasticity of the G protein effector, PDE6 · the same entry in another collection · chain Q against Q, 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 P04972
- Elsewhere: RCSB PDB 3JAB · PDBe 3JAB · UniProt P04972
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