Research workbench
Dimerization domain of xenopus laevis LDB1 in complex with darpin 3
Analyse Dimerization domain of xenopus laevis LDB1 in complex with darpin 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S9T
- Type
- protein
- Length
- 295 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lim domain-binding protein 1; Darpin 3
- UniProt
- P70060
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lim domain-binding protein 1 | protein | 167 | 29% helix, 41% strand | P70060 |
| D | Darpin 3 | protein | 128 | 56% helix, 0% strand | — |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.63 | 0.77 | 30 | empty |
| 2 | 149 | 0.50 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–D · 904 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 6S9T · Dimerization domain of Xenopus laevis LDB1 in complex with darpin 3 · the same entry in another collection · chain A against A, TM-score 1.00
- P70060 · AlphaFold monomer V2.0 prediction for lim domain-binding protein 1 (P70060) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P70060
- Elsewhere: RCSB PDB 6S9T · PDBe 6S9T · UniProt P70060
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