Research workbench
Crystal structure of the complex between the axonemal outer-arm dynein light chain-1 and microtubule binding domain of gamma heavy chain
Analyse Crystal structure of the complex between the axonemal outer-arm dynein light… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L4P
- Type
- protein
- Length
- 333 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein light chain 1, axonemal; Flagellar outer dynein arm heavy chain gamma
- UniProt
- Q9XHH2, A8JFP1
- Ligands
- NA, PO4
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynein light chain 1, axonemal | protein | 195 | 33% helix, 12% strand | Q9XHH2 |
| B | Flagellar outer dynein arm heavy chain gamma | protein | 138 | 65% helix, 6% strand | A8JFP1 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 346 | 0.60 | 0.77 | 44 | empty |
| 2 | 81 | 0.45 | 0.80 | 18 | empty |
| 3 | 53 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1071 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6L4P · Crystal structure of the complex between the axonemal outer-arm dynein light chain-1 and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XHH2 · AlphaFold monomer V2.0 prediction for dynein axonemal light chain 1 (Q9XHH2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9XHH2
- Every structure of UniProt A8JFP1
- Elsewhere: RCSB PDB 6L4P · PDBe 6L4P · UniProt Q9XHH2 · UniProt A8JFP1
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