Research workbench
LCD1 gaf domain in complex with camp ligand
Analyse LCD1 gaf domain in complex with camp ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W10
- Type
- protein
- Length
- 686 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific phosphodiesterase
- UniProt
- Q72MQ6
- Ligands
- CMP
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific phosphodiesterase | protein | 173 | 45% helix, 22% strand | Q72MQ6 |
| B | Cgmp-specific phosphodiesterase | protein | 172 | 45% helix, 22% strand | Q72MQ6 |
| C | Cgmp-specific phosphodiesterase | protein | 171 | 46% helix, 22% strand | Q72MQ6 |
| D | Cgmp-specific phosphodiesterase | protein | 170 | 46% helix, 22% strand | Q72MQ6 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.80 | 0.99 | 24 | CMP |
| 2 | 111 | 0.79 | 0.98 | 24 | CMP |
| 3 | 640 | 0.79 | 0.84 | 89 | empty |
| 4 | 107 | 0.79 | 0.98 | 24 | CMP |
| 5 | 107 | 0.78 | 0.98 | 25 | CMP |
Interfaces
3 interfaces between chains.
- B–C · 1501 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1497 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1001 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 5W10 · Lcd1 GAF domain in complex with cAMP ligand · 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 Q72MQ6
- Elsewhere: RCSB PDB 5W10 · PDBe 5W10 · UniProt Q72MQ6
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