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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
- 3JBQ
- Type
- protein
- Length
- 2,210 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa 2E8 light chain; IGG1-kappa 2E8 heavy chain; Phosphodiesterase 5/6 chimera…
- UniProt
- P04972
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, l | IGG1-kappa 2E8 light chain | protein | 214 | 6% helix, 42% strand | — |
| H, h | IGG1-kappa 2E8 heavy chain | protein | 214 | 1% helix, 41% strand | — |
| B, F | Phosphodiesterase 5/6 chimera catalytic domain | protein | 328 | 66% helix, 0% strand | — |
| D, X | Phosphodiesterase 6 gamma subunit inhibitory peptide | protein | 17 | 41% helix, 0% strand | P04972 |
| C, G | Gafb domain of phosphodiesterase 2A | protein | 161 | 44% helix, 16% strand | — |
| 1, 2 | Gafa domain of cone phosphodiesterase 6C | protein | 171 | 36% helix, 25% strand | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.82 | 0.96 | 34 | empty |
| 2 | 174 | 0.81 | 0.96 | 34 | empty |
| 3 | 803 | 0.76 | 0.80 | 106 | empty |
| 4 | 647 | 0.76 | 0.81 | 72 | empty |
| 5 | 94 | 0.56 | 0.85 | 23 | empty |
Interfaces
19 interfaces between chains.
- l–h · 2281 Ų buried · 38 hydrogen bonds · protein-protein
- L–H · 2281 Ų buried · 37 hydrogen bonds · protein-protein
- 1–2 · 1232 Ų buried · 28 hydrogen bonds · protein-protein
- C–G · 934 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 863 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3JBQ · Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6 · the same entry in another collection · chain 2 against 2, 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 3JBQ · PDBe 3JBQ · UniProt P04972
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