MolNFT v1 · #174895 · protein
E30 F-particle in complex with fcrn
7C9V · VP1: “E30 F-particle in complex with fcrn”. Electron microscopy, 1 ligand (MYR), 20 pockets (best druggability 0.77). MolNFT v1 #174895 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7C9V
- Type
- protein
- Length
- 1,184 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4; IgG receptor fcrn large subunit P51; Beta-2-microglobulin
- UniProt
- Q33C85, P55899, P61769
- Ligands
- MYR
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 6 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 276 | 9% helix, 30% strand | — |
| B | VP2 | protein | 251 | 5% helix, 37% strand | — |
| C | VP3 | protein | 238 | 7% helix, 32% strand | — |
| D | VP4 | protein | 57 | 12% helix, 9% strand | Q33C85 |
| E | IgG receptor fcrn large subunit P51 | protein | 263 | 21% helix, 31% strand | P55899 |
| F | Beta-2-microglobulin | protein | 99 | 0% helix, 45% strand | P61769 |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.77 | 0.82 | 87 | empty |
| 2 | 83 | 0.74 | 0.97 | 23 | empty |
| 3 | 349 | 0.62 | 0.78 | 43 | empty |
| 4 | 59 | 0.62 | 0.91 | 21 | empty |
| 5 | 226 | 0.56 | 0.78 | 32 | empty |
Interfaces
10 interfaces between chains.
- A–C · 4285 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 2128 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1628 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1446 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1236 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid, 1 disulfide (myristoylation, disulfide).
Compared structures
- 7C9V · E30 F-particle in complex with FcRn · the same entry in another collection · chain F against F, TM-score 1.00
- P55899 · AlphaFold monomer V2.0 prediction for IgG receptor fcrn large subunit P51 (P55899) · a predicted model of the same protein · chain E against A, TM-score 0.96
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain F 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 Q33C85
- Every structure of UniProt P55899
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7C9V · PDBe 7C9V · UniProt Q33C85 · UniProt P55899 · UniProt P61769
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