MolNFT v1 · #125617 · protein
Crystal structure of darpin-darpin rigid fusion, variant DD_D12_09_D12
5LE6: “Crystal structure of darpin-darpin rigid fusion, variant DD_D12_09_D12”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.82). MolNFT v1 #125617 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LE6
- Type
- protein
- Length
- 1,770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DD_D12_09_D12
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | DD_D12_09_D12 | protein | 295 | 57% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains D, A, E, C, F
- GOL · Glycerol · additive · 10 copies · chains A, F, E, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.82 | 0.98 | 20 | empty |
| 2 | 151 | 0.82 | 0.97 | 22 | empty |
| 3 | 152 | 0.82 | 0.97 | 23 | empty |
| 4 | 133 | 0.81 | 0.97 | 22 | empty |
| 5 | 127 | 0.81 | 0.98 | 20 | empty |
Interfaces
7 interfaces between chains.
- B–D · 2165 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 2140 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 2133 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1005 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 1005 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5LE6 · Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_09_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 5LE6 · PDBe 5LE6
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