MolNFT v1 · #167158 · protein
Cryo-EM structure of IRP2-FBXL5-SKP1 complex
6VCD · Iron-responsive element binding protein 2, isoform CRA_A: “Cryo-EM structure of IRP2-FBXL5-SKP1 complex”. Electron microscopy, 1 ligand (FES), 5 pockets (best druggability 0.76). MolNFT v1 #167158 on GenesisL1: 3D structure, binding…
- PDB
- 6VCD
- Type
- protein
- Length
- 1,033 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-responsive element binding protein 2, isoform CRA_A; F-BOX/LRR-repeat protein 5…
- UniProt
- D3DW85, Q9UKA1, P63208
- Ligands
- FES
- Pockets
- 5 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 33% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-responsive element binding protein 2, isoform CRA_A | protein | 643 | 32% helix, 14% strand | D3DW85 |
| B | F-BOX/LRR-repeat protein 5 | protein | 255 | 24% helix, 7% strand | Q9UKA1 |
| C | S-phase kinase-associated protein 1 | protein | 135 | 56% helix, 8% strand | P63208 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.76 | 0.78 | 112 | empty |
| 2 | 357 | 0.60 | 0.77 | 46 | empty |
| 3 | 268 | 0.59 | 0.79 | 30 | empty |
| 4 | 174 | 0.56 | 0.81 | 30 | empty |
| 5 | 236 | 0.53 | 0.76 | 32 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1510 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 897 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6VCD · Cryo-EM structure of IRP2-FBXL5-SKP1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKA1 · AlphaFold monomer V2.0 prediction for F-BOX/LRR-repeat protein 5 (Q9UKA1) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 D3DW85
- Every structure of UniProt Q9UKA1
- Every structure of UniProt P63208
- Elsewhere: RCSB PDB 6VCD · PDBe 6VCD · UniProt D3DW85 · UniProt Q9UKA1 · UniProt P63208
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