Research workbench
J22.9-XI: chimeric MOUSE/HUMAN antibody against human bcma (CD269)
Analyse J22.9-XI: chimeric MOUSE/HUMAN antibody against human bcma (CD269) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZFO
- Type
- protein
- Length
- 929 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor superfamily member 17; J22.9-XI Fab, light chain; J22.9-XI…
- UniProt
- Q02223
- Ligands
- CU
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Tumor necrosis factor receptor superfamily member 17 | protein | 36 | 19% helix, 22% strand | Q02223 |
| L | J22.9-XI Fab, light chain | protein | 214 | 5% helix, 48% strand | — |
| H | J22.9-XI Fab, heavy chain | protein | 216 | 7% helix, 54% strand | — |
| B | J22.9-XI Fab, light chain | protein | 213 | 6% helix, 49% strand | — |
| A | J22.9-XI Fab, heavy chain | protein | 215 | 10% helix, 53% strand | — |
| K | Tumor necrosis factor receptor superfamily member 17 | protein | 35 | 20% helix, 23% strand | Q02223 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 3 copies · chains L, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains L, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.67 | 0.74 | 75 | empty |
| 2 | 681 | 0.66 | 0.75 | 54 | empty |
| 3 | 245 | 0.51 | 0.75 | 34 | empty |
| 4 | 113 | 0.37 | 0.74 | 23 | empty |
| 5 | 65 | 0.31 | 0.75 | 15 | empty |
Interfaces
7 interfaces between chains.
- B–A · 1785 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1749 Ų buried · 13 hydrogen bonds · protein-protein
- H–A · 856 Ų buried · 14 hydrogen bonds · protein-protein
- L–K · 503 Ų buried · 6 hydrogen bonds · protein-protein
- F–B · 484 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4ZFO · J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269) · the same entry in another collection · chain K against K, TM-score 1.00
- Q02223 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain K against A, TM-score 0.89
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 Q02223
- Elsewhere: RCSB PDB 4ZFO · PDBe 4ZFO · UniProt Q02223
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