MolNFT v1 · #158009 · protein
Crystal structure of SYNT001, a human fcrn blocking monoclonal antibody
6NHA · IgG receptor fcrn large subunit P51: “Crystal structure of SYNT001, a human fcrn blocking monoclonal antibody”. X-ray diffraction, 11 pockets (best druggability 0.69). MolNFT v1 #158009 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NHA
- Type
- protein
- Length
- 778 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; SYNT001-Fab light chain…
- UniProt
- P55899, P61769
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IgG receptor fcrn large subunit P51 | protein | 256 | 24% helix, 43% strand | P55899 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| L | SYNT001-Fab light chain | protein | 212 | 5% helix, 50% strand | — |
| H | SYNT001-Fab heavy chain | protein | 211 | 6% helix, 49% strand | — |
Ligands and binding sites
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 3 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.69 | 0.86 | 28 | NHE |
| 2 | 503 | 0.64 | 0.76 | 38 | empty |
| 3 | 377 | 0.56 | 0.75 | 48 | empty |
| 4 | 109 | 0.56 | 0.84 | 20 | empty |
| 5 | 185 | 0.50 | 0.77 | 22 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1679 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1530 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 530 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 198 Ų buried · 2 hydrogen bonds · protein-protein
- A–L · 189 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6NHA · Crystal structure of SYNT001, a human FcRn blocking monoclonal antibody · the same entry in another collection · chain A 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 B against A, TM-score 0.98
- P55899 · AlphaFold monomer V2.0 prediction for IgG receptor fcrn large subunit P51 (P55899) · a predicted model of the same protein · chain A 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 P55899
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6NHA · PDBe 6NHA · UniProt P55899 · UniProt P61769
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