Research workbench
Structure of human ferroportin bound to hepcidin and cobalt in lipid nanodisc
Analyse Structure of human ferroportin bound to hepcidin and cobalt in lipid nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WBV
- Type
- protein
- Length
- 892 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepcidin; Solute carrier family 40 member 1; FAB45D8 light chain; FAB45D8 heavy chain
- EC
- 7.-.-.-
- UniProt
- P81172, Q9NP59
- Ligands
- AGA, CO
- Pockets
- 7 · best druggability 0.89
Structure
electron microscopy · 4 distinct chains · 43% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Hepcidin | protein | 25 | 0% helix, 40% strand | P81172 |
| A | Solute carrier family 40 member 1 (EC 7.-.-.-) | protein | 429 | 85% helix, 0% strand | Q9NP59 |
| L | FAB45D8 light chain | protein | 218 | 6% helix, 53% strand | — |
| H | FAB45D8 heavy chain | protein | 220 | 4% helix, 52% strand | — |
Ligands and binding sites
- AGA · (1S)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(pentanoyloxy)methyl]ethyl octanoate · ligand · 2 copies · chains A
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.89 | 0.92 | 87 | CO |
| 2 | 459 | 0.63 | 0.76 | 59 | empty |
| 3 | 301 | 0.51 | 0.74 | 38 | empty |
| 4 | 186 | 0.46 | 0.75 | 25 | empty |
| 5 | 68 | 0.37 | 0.78 | 18 | empty |
Interfaces
4 interfaces between chains.
- L–H · 2079 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 1296 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 375 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 284 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6WBV · Structure of human ferroportin bound to hepcidin and cobalt in lipid nanodisc · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NP59 · AlphaFold monomer V2.0 prediction for solute carrier family 40 member 1 (Q9NP59) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P81172 · AlphaFold monomer V2.0 prediction for hepcidin (P81172) · a predicted model of the same protein · chain B against A, TM-score 0.54
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 P81172
- Every structure of UniProt Q9NP59
- Elsewhere: RCSB PDB 6WBV · PDBe 6WBV · UniProt P81172 · UniProt Q9NP59
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