Research workbench
Crystal structure of an extracellular domain fragment of human baff
Analyse Crystal structure of an extracellular domain fragment of human baff in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KD7
- Type
- protein
- Length
- 864 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 13B
- UniProt
- Q9Y275
- Pockets
- 11 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, K, L, M | Tumor necrosis factor ligand superfamily member 13B | protein | 144 | 0% helix, 53% strand | Q9Y275 |
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.51 | 0.78 | 26 | empty |
| 2 | 160 | 0.48 | 0.77 | 24 | empty |
| 3 | 123 | 0.41 | 0.75 | 19 | empty |
| 4 | 111 | 0.41 | 0.75 | 17 | empty |
| 5 | 96 | 0.39 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- L–M · 986 Ų buried · 23 hydrogen bonds · protein-protein
- K–M · 984 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 978 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 977 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 976 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1KD7 · Crystal structure of an extracellular domain fragment of human BAFF · the same entry in another collection · chain C against C, TM-score 1.00
- Q9Y275 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 13B… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9Y275
- Elsewhere: RCSB PDB 1KD7 · PDBe 1KD7 · UniProt Q9Y275
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