Research workbench
Crystal structure of ISL1 lim domains with LDB1 lim-interaction domain
Analyse Crystal structure of ISL1 lim domains with LDB1 lim-interaction domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JCJ
- Type
- protein
- Length
- 442 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin gene enhancer protein isl-1,LIM domain-binding protein 1
- UniProt
- P61372, P70662
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin gene enhancer protein isl-1,LIM domain-binding protein 1 | protein | 144 | 11% helix, 36% strand | P61372, P70662 |
| B | Insulin gene enhancer protein isl-1,LIM domain-binding protein 1 | protein | 148 | 11% helix, 32% strand | P61372, P70662 |
| C | Insulin gene enhancer protein isl-1,LIM domain-binding protein 1 | protein | 150 | 12% helix, 34% strand | P61372, P70662 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.35 | 0.72 | 19 | empty |
| 2 | 59 | 0.30 | 0.75 | 18 | empty |
| 3 | 66 | 0.30 | 0.74 | 13 | empty |
| 4 | 63 | 0.28 | 0.73 | 18 | empty |
| 5 | 59 | 0.28 | 0.74 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–B · 355 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 214 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4JCJ · Crystal structure of Isl1 LIM domains with Ldb1 LIM-interaction domain · the same entry in another collection · chain A against A, TM-score 1.00
- P61372 · AlphaFold monomer V2.0 prediction for insulin gene enhancer protein isl-1 (P61372) · a predicted model of the same protein · chain C against A, TM-score 0.88
- P70662 · AlphaFold monomer V2.0 prediction for lim domain-binding protein 1 (P70662) · a predicted model of the same protein · chain A against A, TM-score 0.30
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 P61372
- Every structure of UniProt P70662
- Elsewhere: RCSB PDB 4JCJ · PDBe 4JCJ · UniProt P61372 · UniProt P70662
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