Research workbench
Crystal structure of DYNLT1/TCTEX-1 in complex with ARHGEF2
Analyse Crystal structure of DYNLT1/TCTEX-1 in complex with ARHGEF2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WI4
- Type
- protein
- Length
- 375 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein light chain tctex-type 1,RHO guanine nucleotide exchange factor 2
- UniProt
- P51807, Q60875
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynein light chain tctex-type 1,RHO guanine nucleotide exchange factor 2 | protein | 125 | 32% helix, 36% strand | P51807, Q60875 |
| B | Dynein light chain tctex-type 1,RHO guanine nucleotide exchange factor 2 | protein | 125 | 30% helix, 40% strand | P51807, Q60875 |
| C | Dynein light chain tctex-type 1,RHO guanine nucleotide exchange factor 2 | protein | 125 | 33% helix, 32% strand | P51807, Q60875 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.72 | 0.98 | 25 | empty |
| 2 | 179 | 0.47 | 0.76 | 21 | empty |
| 3 | 164 | 0.42 | 0.74 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1742 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 148 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WI4 · Crystal structure of DYNLT1/TCTEX-1 in complex with ARHGEF2 · the same entry in another collection · chain A against A, TM-score 1.00
- P51807 · AlphaFold monomer V2.0 prediction for dynein light chain tctex-type 1 (P51807) · a predicted model of the same protein · chain A against A, TM-score 0.82
- Q60875 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 2 (Q60875) · a predicted model of the same protein · chain C against A, TM-score 0.35
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 P51807
- Every structure of UniProt Q60875
- Elsewhere: RCSB PDB 5WI4 · PDBe 5WI4 · UniProt P51807 · UniProt Q60875
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