Research workbench
Cryo-EM structure of SLC40/FERROPORTIN in complex with Fab
Analyse Cryo-EM structure of SLC40/FERROPORTIN in complex with Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VYH
- Type
- protein
- Length
- 860 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Solute carrier family 40 protein; 11F9 light-chain; 11F9 heavy-chain
- UniProt
- A0A1U7U6F1
- Ligands
- CO
- Pockets
- 14 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Solute carrier family 40 protein | protein | 428 | 69% helix, 0% strand | A0A1U7U6F1 |
| C | 11F9 light-chain | protein | 213 | 4% helix, 40% strand | — |
| D | 11F9 heavy-chain | protein | 219 | 5% helix, 46% strand | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.84 | 0.85 | 96 | CO |
| 2 | 561 | 0.69 | 0.79 | 84 | empty |
| 3 | 429 | 0.68 | 0.80 | 65 | empty |
| 4 | 295 | 0.63 | 0.80 | 32 | empty |
| 5 | 265 | 0.60 | 0.80 | 43 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1189 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 857 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6VYH · Cryo-EM structure of SLC40/ferroportin in complex with Fab · the same entry in another collection · chain C against C, TM-score 1.00
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 A0A1U7U6F1
- Elsewhere: RCSB PDB 6VYH · PDBe 6VYH · UniProt A0A1U7U6F1
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