Research workbench
Crystal structure of fcrn bound to ucb-84
Analyse Crystal structure of fcrn bound to ucb-84 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C98
- Type
- protein
- Length
- 722 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgG receptor fcrn large subunit P51; Beta-2-microglobulin
- UniProt
- P55899, P61769
- Ligands
- CYS, ER7
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | IgG receptor fcrn large subunit P51 | protein | 262 | 27% helix, 43% strand | P55899 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- CYS · Cysteine · ligand · 2 copies · chains A, B, C, D
- ER7 · 1-[7-(3-fluorophenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]ethan-1-one · ligand · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
- PEG · Di(hydroxyethyl)ether · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.82 | 0.83 | 117 | ER7, PEG, CYS |
| 2 | 84 | 0.53 | 0.85 | 25 | empty |
| 3 | 217 | 0.53 | 0.77 | 32 | empty |
| 4 | 226 | 0.51 | 0.76 | 29 | empty |
| 5 | 52 | 0.29 | 0.76 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1481 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1469 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 796 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 128 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 113 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6C98 · Crystal structure of FcRn bound to UCB-84 · the same entry in another collection · chain C against C, 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 C against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P55899
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6C98 · PDBe 6C98 · UniProt P55899 · UniProt P61769
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