Research workbench
Crystal structure of darpin-darpin rigid fusion, variant DD_D12_13_D12
Analyse Crystal structure of darpin-darpin rigid fusion, variant DD_D12_13_D12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LE7
- Type
- protein
- Length
- 1,267 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DD_D12_13_D12
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DD_D12_13_D12 | protein | 316 | 57% helix, 0% strand | — |
| B | DD_D12_13_D12 | protein | 317 | 56% helix, 0% strand | — |
| C | DD_D12_13_D12 | protein | 318 | 56% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.65 | 0.75 | 58 | SO4 |
| 2 | 685 | 0.65 | 0.75 | 64 | empty |
| 3 | 270 | 0.60 | 0.79 | 35 | empty |
| 4 | 404 | 0.59 | 0.75 | 37 | empty |
| 5 | 133 | 0.48 | 0.78 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–C · 660 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 452 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 318 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 301 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 232 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5LE7 · Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_13_D12 · 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 5LE7 · PDBe 5LE7
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