Research workbench
Complex between baff and a BR3 derived peptide presented in a beta-hairpin scaffold
Analyse Complex between baff and a BR3 derived peptide presented in a beta-hairpin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OSG
- Type
- protein
- Length
- 936 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 13B; BR3 derived peptide
- UniProt
- Q9Y275
- Ligands
- MG
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Tumor necrosis factor ligand superfamily member 13B | protein | 144 | 0% helix, 56% strand | Q9Y275 |
| G, J, H, I, K, L | BR3 derived peptide | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.72 | 0.94 | 20 | empty |
| 2 | 159 | 0.53 | 0.80 | 22 | MG |
| 3 | 151 | 0.49 | 0.79 | 27 | MG |
| 4 | 168 | 0.45 | 0.75 | 22 | empty |
| 5 | 170 | 0.42 | 0.74 | 32 | empty |
Interfaces
23 interfaces between chains.
- B–C · 1036 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 1021 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 1017 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1001 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 1000 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1OSG · Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q9Y275
- Elsewhere: RCSB PDB 1OSG · PDBe 1OSG · UniProt Q9Y275
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