Research workbench
Crystal structure of neural ectodermal development factor imp-L2.
Analyse Crystal structure of neural ectodermal development factor imp-L2. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CBP
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NEURAL/ECTODERMAL development factor imp-L2
- UniProt
- Q09024
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NEURAL/ECTODERMAL development factor imp-L2 | protein | 207 | 3% helix, 51% strand | Q09024 |
| B | NEURAL/ECTODERMAL development factor imp-L2 | protein | 206 | 1% helix, 52% strand | Q09024 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.59 | 0.80 | 28 | GOL |
| 2 | 341 | 0.58 | 0.76 | 34 | empty |
| 3 | 140 | 0.41 | 0.74 | 24 | empty |
| 4 | 51 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 4CBP · Crystal structure of neural ectodermal development factor IMP-L2. · the same entry in another collection · chain A against A, TM-score 1.00
- Q09024 · AlphaFold monomer V2.0 prediction for NEURAL/ECTODERMAL development factor imp-L2 (Q09024) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q09024
- Elsewhere: RCSB PDB 4CBP · PDBe 4CBP · UniProt Q09024
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