MolNFT v1 · #179224 · protein
Crystal structure of broadly plasmodium rifin reactive LAIR1-inserted antibody MGD21
7JZ4 · MGD21 heavy chain: “Crystal structure of broadly plasmodium rifin reactive LAIR1-inserted antibody MGD21”. X-ray diffraction, 2 ligands (NAG, PO4), 14 pockets (best druggability 0.69). MolNFT v1 #179224 on GenesisL1: 3D structure…
- PDB
- 7JZ4
- Type
- protein
- Length
- 1,109 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MGD21 heavy chain; MGD21 light chain
- Ligands
- NAG, PO4
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MGD21 heavy chain | protein | 355 | 3% helix, 49% strand | — |
| B, D | MGD21 light chain | protein | 213 | 7% helix, 50% strand | — |
| C | MGD21 heavy chain | protein | 328 | 2% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, C, A, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.69 | 0.82 | 57 | empty |
| 2 | 406 | 0.67 | 0.80 | 50 | empty |
| 3 | 93 | 0.66 | 0.91 | 28 | empty |
| 4 | 424 | 0.63 | 0.77 | 47 | empty |
| 5 | 168 | 0.59 | 0.83 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2406 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 2086 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 367 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 261 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7JZ4 · Crystal structure of broadly Plasmodium RIFIN reactive LAIR1-inserted antibody MGD21 · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 7JZ4 · PDBe 7JZ4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.