Research workbench
Crystal structure of murine nk cell ligand rae-1 beta
Analyse Crystal structure of murine nk cell ligand rae-1 beta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JFM
- Type
- protein
- Length
- 870 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid early transcript beta
- UniProt
- O08603
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Retinoic acid early transcript beta | protein | 174 | 34% helix, 27% strand | O08603 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.72 | 0.80 | 57 | empty |
| 2 | 684 | 0.66 | 0.75 | 74 | empty |
| 3 | 230 | 0.60 | 0.80 | 44 | empty |
| 4 | 179 | 0.52 | 0.78 | 22 | empty |
| 5 | 275 | 0.52 | 0.75 | 28 | empty |
Interfaces
4 interfaces between chains.
- B–C · 573 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 473 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 427 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 390 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1JFM · Crystal structure of murine nk cell ligand rae-1 beta · the same entry in another collection · chain A against A, TM-score 1.00
- O08603 · AlphaFold monomer V2.0 prediction for retinoic acid early-inducible protein 1-beta… · 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 O08603
- Elsewhere: RCSB PDB 1JFM · PDBe 1JFM · UniProt O08603
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