Research workbench
AKAP13 (akap-lbc) rhogef domain in complex with rhoa
Analyse AKAP13 (akap-lbc) rhogef domain in complex with rhoa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D0N
- Type
- protein
- Length
- 550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming protein rhoa; A-kinase anchor protein 13
- EC
- 3.6.5.2
- UniProt
- P61586, Q12802
- Ligands
- GDP, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transforming protein rhoa (EC 3.6.5.2) | protein | 179 | 37% helix, 23% strand | P61586 |
| B | A-kinase anchor protein 13 | protein | 371 | 59% helix, 16% strand | Q12802 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.70 | 0.81 | 46 | empty |
| 2 | 236 | 0.59 | 0.79 | 30 | EDO |
| 3 | 298 | 0.55 | 0.76 | 38 | GDP |
| 4 | 104 | 0.38 | 0.75 | 22 | empty |
| 5 | 57 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1508 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
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 P61586
- Every structure of UniProt Q12802
- Elsewhere: RCSB PDB 4D0N · PDBe 4D0N · UniProt P61586 · UniProt Q12802
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