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Crystal structure of the human tsg-6 link module
Analyse Crystal structure of the human tsg-6 link module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PF5
- Type
- protein
- Length
- 456 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor-inducible protein tsg-6
- UniProt
- P98066
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor-inducible protein tsg-6 | protein | 88 | 25% helix, 34% strand | P98066 |
| B | Tumor necrosis factor-inducible protein tsg-6 | protein | 94 | 23% helix, 30% strand | P98066 |
| C | Tumor necrosis factor-inducible protein tsg-6 | protein | 93 | 24% helix, 32% strand | P98066 |
| D | Tumor necrosis factor-inducible protein tsg-6 | protein | 96 | 26% helix, 33% strand | P98066 |
| E | Tumor necrosis factor-inducible protein tsg-6 | protein | 85 | 25% helix, 33% strand | P98066 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, A, E
- 2PE · Nonaethylene glycol · additive · 5 copies · chains B, D, A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.71 | 0.82 | 36 | 2PE |
| 2 | 113 | 0.37 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 404 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 382 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 380 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 326 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 308 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 P98066
- Elsewhere: RCSB PDB 2PF5 · PDBe 2PF5 · UniProt P98066
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