Research workbench
Structure of human insulin cocrystallized with protamine and urea
Analyse Structure of human insulin cocrystallized with protamine and urea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OMG
- Type
- protein
- Length
- 147 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin a chain; Insulin B chain
- UniProt
- P01308
- Ligands
- URE, ARF, CRS, NA, ZN, CL
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Insulin a chain | protein | 21 | 48% helix, 5% strand | P01308 |
| B, D, F | Insulin B chain | protein | 28 | 75% helix, 4% strand | P01308 |
Ligands and binding sites
- URE · Urea · ligand · 6 copies · chains A, B, D, E, F, C
- ARF · Formamide · ligand · 5 copies · chains A, B, E, D, C, F
- CRS · M-cresol · ligand · 3 copies · chains A, B, D, C, F, E
- NA · Sodium ion · metal · chains A
- ZN · Zinc ion · metal · chains B, D, F
- CL · Chloride ion · ion · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.50 | 0.83 | 15 | CRS |
| 2 | 87 | 0.47 | 0.81 | 15 | CRS |
| 3 | 79 | 0.46 | 0.81 | 16 | CRS |
| 4 | 76 | 0.43 | 0.80 | 18 | CL, URE |
Interfaces
9 interfaces between chains.
- E–F · 576 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 556 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 526 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 163 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 150 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 2OMG · Structure of human insulin cocrystallized with protamine and urea · 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 2OMG · PDBe 2OMG · UniProt P01308
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