Research workbench
High resolution X-ray crystal structure of synthetic insulin lispro
Analyse High resolution X-ray crystal structure of synthetic insulin lispro in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UDP
- Type
- protein
- Length
- 291 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin lispro a chain; Insulin lispro B chain
- UniProt
- P01308
- Ligands
- IPH, ZN, NA, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 72% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Insulin lispro a chain | protein | 21 | 48% helix, 5% strand | P01308 |
| B, F | Insulin lispro B chain | protein | 29 | 72% helix, 10% strand | P01308 |
| D, J | Insulin lispro B chain | protein | 26 | 81% helix, 8% strand | P01308 |
| H | Insulin lispro B chain | protein | 27 | 78% helix, 11% strand | P01308 |
| L | Insulin lispro B chain | protein | 28 | 75% helix, 11% strand | P01308 |
Ligands and binding sites
- IPH · Phenol · ligand · 6 copies · chains A, B, D, J, C, F, E, H, L, G, I, K
- ZN · Zinc ion · metal · 2 copies · chains B, H, J, D, F, L
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 2 copies · chains B, H, J, D, F, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.80 | 0.94 | 31 | IPH |
| 2 | 290 | 0.78 | 0.90 | 55 | IPH |
| 3 | 260 | 0.77 | 0.89 | 43 | IPH |
| 4 | 121 | 0.45 | 0.78 | 25 | CL |
| 5 | 112 | 0.45 | 0.78 | 22 | empty |
Interfaces
39 interfaces between chains.
- B–F · 737 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 685 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 548 Ų buried · 4 hydrogen bonds · protein-protein
- D–J · 547 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 5UDP · High resolution x-ray crystal structure of synthetic insulin lispro · 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
- Every structure of UniProt P01308
- Elsewhere: RCSB PDB 5UDP · PDBe 5UDP · UniProt P01308
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