MolNFT v1 · #185637 · protein
Magacizumab Fab fragment in complex with human LRG1 epitope
7Q4Q · Magacizumab light chain: “Magacizumab Fab fragment in complex with human LRG1 epitope”. X-ray diffraction, 8 pockets (best druggability 0.57). MolNFT v1 #185637 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7Q4Q
- Type
- protein
- Length
- 904 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Magacizumab light chain; Magacizumab heavy chain; LRG1 epitope
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Magacizumab light chain | protein | 218 | 6% helix, 51% strand | — |
| B, D | Magacizumab heavy chain | protein | 219 | 8% helix, 52% strand | — |
| E, F | LRG1 epitope | protein | 15 | 27% helix, 0% strand | — |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.57 | 0.81 | 40 | empty |
| 2 | 307 | 0.51 | 0.74 | 40 | empty |
| 3 | 101 | 0.48 | 0.80 | 19 | empty |
| 4 | 142 | 0.48 | 0.78 | 27 | empty |
| 5 | 130 | 0.46 | 0.78 | 20 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1883 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1871 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 410 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 409 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7Q4Q · Magacizumab Fab fragment in complex with human LRG1 epitope · 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 7Q4Q · PDBe 7Q4Q
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