Research workbench
Structure of human insulin cocrystallized with protamine
Analyse Structure of human insulin cocrystallized with protamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OMI
- Type
- protein
- Length
- 297 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin a chain; Insulin B chain
- UniProt
- P01308
- Ligands
- RCO, ZN, CL
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Insulin a chain | protein | 21 | 57% helix, 5% strand | P01308 |
| B | Insulin B chain | protein | 30 | 70% helix, 10% strand | P01308 |
| D | Insulin B chain | protein | 29 | 69% helix, 10% strand | P01308 |
| F, H, J, L | Insulin B chain | protein | 28 | 64% helix, 11% strand | P01308 |
Ligands and binding sites
- RCO · Resorcinol · ligand · 6 copies · chains A, B, D, H, C, F, L, E, J, G, I, K
- ZN · Zinc ion · metal · 2 copies · chains B, D, F, H, J, L
- CL · Chloride ion · ion · 2 copies · chains B, D, F, H, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.83 | 0.86 | 95 | RCO |
| 2 | 157 | 0.65 | 0.86 | 29 | RCO |
| 3 | 120 | 0.59 | 0.84 | 26 | RCO |
| 4 | 146 | 0.58 | 0.83 | 30 | RCO |
| 5 | 76 | 0.44 | 0.80 | 21 | ZN, CL |
Interfaces
38 interfaces between chains.
- D–H · 717 Ų buried · 11 hydrogen bonds · protein-protein
- B–J · 704 Ų buried · 14 hydrogen bonds · protein-protein
- F–L · 662 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 587 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 2OMI · Structure of human insulin cocrystallized with protamine · 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 2OMI · PDBe 2OMI · UniProt P01308
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