MolNFT v1 · #167388 · protein
Structure of CD20 in complex with rituximab Fab
6VJA · B-lymphocyte antigen CD20: “Structure of CD20 in complex with rituximab Fab”. Electron microscopy, 1 ligand (Y01), 13 pockets (best druggability 0.86). MolNFT v1 #167388 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VJA
- Type
- protein
- Length
- 1,204 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-lymphocyte antigen CD20; Rituximab Fab heavy chain; Rituximab Fab light chain
- UniProt
- P11836
- Ligands
- Y01
- Pockets
- 13 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | B-lymphocyte antigen CD20 | protein | 165 | 64% helix, 0% strand | P11836 |
| H, I | Rituximab Fab heavy chain | protein | 224 | 10% helix, 54% strand | — |
| L, M | Rituximab Fab light chain | protein | 213 | 6% helix, 49% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 6 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.86 | 0.88 | 86 | empty |
| 2 | 108 | 0.59 | 0.86 | 25 | empty |
| 3 | 218 | 0.57 | 0.79 | 40 | empty |
| 4 | 104 | 0.56 | 0.85 | 25 | empty |
| 5 | 193 | 0.48 | 0.75 | 40 | empty |
Interfaces
14 interfaces between chains.
- H–L · 2044 Ų buried · 9 hydrogen bonds · protein-protein
- I–M · 2031 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1620 Ų buried · 1 hydrogen bond · protein-protein
- H–I · 352 Ų buried · 0 hydrogen bonds · protein-protein
- D–I · 348 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
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 P11836
- Elsewhere: RCSB PDB 6VJA · PDBe 6VJA · UniProt P11836
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.