Research workbench
Crystal structure of gef domain of dennd 1A in complex with rab GTPase RAB35-GDP bound state.
Analyse Crystal structure of gef domain of dennd 1A in complex with rab GTPase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EKK
- Type
- protein
- Length
- 1,106 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Denn domain-containing protein 1A; RAS-related protein rab-35
- UniProt
- Q8TEH3, Q15286
- Ligands
- GDP, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Denn domain-containing protein 1A | protein | 375 | 43% helix, 18% strand | Q8TEH3 |
| B | Denn domain-containing protein 1A | protein | 381 | 42% helix, 19% strand | Q8TEH3 |
| C | RAS-related protein rab-35 | protein | 176 | 40% helix, 27% strand | Q15286 |
| D | RAS-related protein rab-35 | protein | 174 | 34% helix, 28% strand | Q15286 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.78 | 0.83 | 59 | EDO |
| 2 | 648 | 0.77 | 0.82 | 61 | EDO |
| 3 | 101 | 0.41 | 0.77 | 21 | SO4 |
| 4 | 57 | 0.37 | 0.79 | 21 | SO4 |
| 5 | 56 | 0.36 | 0.79 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1464 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1434 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6EKK · Crystal structure of GEF domain of DENND 1A in complex with Rab GTPase Rab35-GDP bound… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8TEH3 · AlphaFold monomer V2.0 prediction for denn domain-containing protein 1A (Q8TEH3) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q15286 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-35 (Q15286) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 Q8TEH3
- Every structure of UniProt Q15286
- Elsewhere: RCSB PDB 6EKK · PDBe 6EKK · UniProt Q8TEH3 · UniProt Q15286
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.