MolNFT v1 · #5678 · protein
Structure of the epididymal retinoic acid-binding protein at 2.1 ångströms resolution
1EPB: “Structure of the epididymal retinoic acid-binding protein at 2.1 ångströms resolution”. X-ray diffraction, 1 ligand (9CR), 5 pockets (best druggability 0.78). MolNFT v1 #5678 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1EPB
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epididymal retinoic acid-binding protein
- UniProt
- P06911
- Ligands
- 9CR
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epididymal retinoic acid-binding protein | protein | 160 | 17% helix, 49% strand | P06911 |
| B | Epididymal retinoic acid-binding protein | protein | 164 | 18% helix, 42% strand | P06911 |
Ligands and binding sites
- 9CR · (9cis)-retinoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.78 | 0.85 | 42 | 9CR |
| 2 | 478 | 0.77 | 0.84 | 45 | 9CR |
| 3 | 313 | 0.66 | 0.81 | 45 | empty |
| 4 | 52 | 0.36 | 0.80 | 14 | empty |
| 5 | 57 | 0.32 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1EPB · Structure of the epididymal retinoic acid-binding protein at 2.1 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P06911 · AlphaFold monomer V2.0 prediction for epididymal-specific lipocalin-5 (P06911) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P06911
- Elsewhere: RCSB PDB 1EPB · PDBe 1EPB · UniProt P06911
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