MolNFT v1 · #168307 · protein
Structure of human ferroportin bound to hepcidin and cobalt in lipid nanodisc
6WBV: “Structure of human ferroportin bound to hepcidin and cobalt in lipid nanodisc”. Electron microscopy, 2 ligands (AGA, CO), 7 pockets (best druggability 0.89). MolNFT v1 #168307 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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