Research workbench
Crystal structure of anti-il-13 darpin 6G9
Analyse Crystal structure of anti-il-13 darpin 6G9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KNG
- Type
- protein
- Length
- 626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Darpin 6G9
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Darpin 6G9 | protein | 158 | 55% helix, 0% strand | — |
| B | Darpin 6G9 | protein | 159 | 55% helix, 0% strand | — |
| D | Darpin 6G9 | protein | 151 | 54% helix, 0% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.80 | 0.81 | 65 | empty |
| 2 | 328 | 0.50 | 0.73 | 45 | PO4 |
| 3 | 154 | 0.44 | 0.75 | 24 | empty |
| 4 | 54 | 0.26 | 0.73 | 17 | empty |
| 5 | 52 | 0.26 | 0.73 | 18 | GOL |
Interfaces
4 interfaces between chains.
- A–D · 480 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 457 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 394 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 277 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KNG · Crystal structure of anti-il-13 darpin 6G9 · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 5KNG · PDBe 5KNG
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