MolNFT v1 · #81862 · protein
Re-refinement of pdb entry 1OSG - complex between baff and a BR3 derived peptide presented in a beta-hairpin scaffold - reveals an additonal copy of the peptide.
3V56 · Tumor necrosis factor ligand superfamily member 13B: “Re-refinement of pdb entry 1OSG - complex between baff and a BR3 derived peptide presented in a beta-hairpin…”. X-ray diffraction, 3 ligands (ACE, NH2, SO4), 9 pockets (best…
- PDB
- 3V56
- Type
- protein
- Length
- 948 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 13B; BR3 derived peptive
- UniProt
- Q9Y275
- Ligands
- ACE, NH2, SO4
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 52% 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, 52% strand | Q9Y275 |
| G, H, I, J, K, L, Z | BR3 derived peptive | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains G
- NH2 · Amino group · ion · 7 copies · chains G, H, I, J, K, L, E, Z
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.67 | 0.91 | 18 | empty |
| 2 | 143 | 0.51 | 0.80 | 24 | SO4 |
| 3 | 112 | 0.46 | 0.80 | 19 | SO4 |
| 4 | 112 | 0.40 | 0.75 | 17 | empty |
| 5 | 118 | 0.40 | 0.75 | 19 | empty |
Interfaces
25 interfaces between chains.
- D–E · 1020 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1013 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 993 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 984 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 983 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3V56 · Re-refinement of PDB entry 1OSG - Complex between BAFF and a BR3 derived peptide… · the same entry in another collection · chain Z against Z, 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 3V56 · PDBe 3V56 · UniProt Q9Y275
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