Research workbench
The crystal structure of april bound to bcma
Analyse The crystal structure of april bound to bcma in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XU2
- Type
- protein
- Length
- 519 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 13; Tumor necrosis factor receptor…
- UniProt
- Q9D777, Q02223
- Ligands
- NI
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Tumor necrosis factor ligand superfamily member 13 | protein | 137 | 2% helix, 62% strand | Q9D777 |
| R | Tumor necrosis factor receptor superfamily member 17 | protein | 36 | 31% helix, 22% strand | Q02223 |
| S | Tumor necrosis factor receptor superfamily member 17 | protein | 37 | 22% helix, 22% strand | Q02223 |
| T | Tumor necrosis factor receptor superfamily member 17 | protein | 35 | 11% helix, 23% strand | Q02223 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.56 | 0.78 | 33 | empty |
| 2 | 75 | 0.42 | 0.80 | 15 | empty |
| 3 | 78 | 0.38 | 0.77 | 13 | empty |
| 4 | 97 | 0.38 | 0.76 | 22 | empty |
| 5 | 87 | 0.37 | 0.76 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–D · 995 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 981 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 933 Ų buried · 17 hydrogen bonds · protein-protein
- B–S · 693 Ų buried · 8 hydrogen bonds · protein-protein
- A–R · 685 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1XU2 · The crystal structure of APRIL bound to BCMA · the same entry in another collection · chain T against T, TM-score 1.00
- Q9D777 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 13… · a predicted model of the same protein · chain A against A, 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 R against A, TM-score 0.85
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 Q9D777
- Every structure of UniProt Q02223
- Elsewhere: RCSB PDB 1XU2 · PDBe 1XU2 · UniProt Q9D777 · UniProt Q02223
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