Research workbench
Sp-2CL-camps bound to pkar CBD2
Analyse Sp-2CL-camps bound to pkar CBD2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T3N
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase regulatory subunit
- EC
- 2.7.11.11
- UniProt
- Q7KQK0
- Ligands
- 75G, IOD
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase regulatory subunit (EC 2.7.11.11) | protein | 153 | 39% helix, 25% strand | Q7KQK0 |
| B | Camp-dependent protein kinase regulatory subunit (EC 2.7.11.11) | protein | 146 | 36% helix, 27% strand | Q7KQK0 |
Ligands and binding sites
- 75G · (2S,4aR,6R,7R,7aS)-6-(6-amino-2-chloro-9H-purin-9-yl)-7-hydroxy-2-sulfanyltetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-2-one · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.73 | 0.89 | 33 | 75G |
| 2 | 247 | 0.73 | 0.87 | 39 | 75G |
| 3 | 131 | 0.40 | 0.74 | 21 | empty |
| 4 | 65 | 0.31 | 0.75 | 13 | IOD |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5T3N · Sp-2Cl-cAMPS bound to PKAR CBD2 · 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 Q7KQK0
- Elsewhere: RCSB PDB 5T3N · PDBe 5T3N · UniProt Q7KQK0
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