Research workbench
Structure of human insulin in presence of thiocyanate at pH 6.5
Analyse Structure of human insulin in presence of thiocyanate at pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OM1
- Type
- protein
- Length
- 902 residues
- Chains
- 36
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin a chain; Insulin B chain
- UniProt
- P01308
- Ligands
- RCO, ZN, SCN
- Pockets
- 11 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, Q, S, U, X, 1, 3, a, c, e, g, i, k | Insulin a chain | protein | 21 | 57% helix, 5% strand | P01308 |
| B, D, F, H, L, V, Y, 2, 4, b, d, f, h, j | Insulin B chain | protein | 29 | 69% helix, 10% strand | P01308 |
| J, R, T | Insulin B chain | protein | 30 | 67% helix, 10% strand | P01308 |
| l | Insulin B chain | protein | 28 | 71% helix, 11% strand | P01308 |
Ligands and binding sites
- RCO · Resorcinol · ligand · 18 copies · chains A, B, F, H, C, D, J, L, E, G, I, K, Q, R, T, 2, S, V, 4, U, Y, X, 1, 3, a, b, f, j, c, d, l, e, h, g, i, k
- ZN · Zinc ion · metal · 6 copies · chains B, F, J, D, H, L, R, T, V, Y, 2, 4, b, d, f, h, j, l
- SCN · Thiocyanate ion · ion · 6 copies · chains B, F, J, D, H, L, R, T, V, Y, 2, 4, b, d, f, h, j, l
- GOL · Glycerol · additive · chains Q, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.89 | 0.94 | 94 | RCO |
| 2 | 485 | 0.87 | 0.94 | 66 | RCO |
| 3 | 618 | 0.87 | 0.92 | 96 | RCO |
| 4 | 192 | 0.68 | 0.86 | 28 | RCO |
| 5 | 226 | 0.60 | 0.80 | 35 | RCO |
Interfaces
131 interfaces between chains.
- d–h · 762 Ų buried · 16 hydrogen bonds · protein-protein
- V–4 · 735 Ų buried · 12 hydrogen bonds · protein-protein
- R–Y · 730 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 729 Ų buried · 14 hydrogen bonds · protein-protein
- T–2 · 722 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide (disulfide).
Compared structures
- 2OM1 · Structure of human insulin in presence of thiocyanate at pH 6.5 · the same entry in another collection · chain B against B, 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 2OM1 · PDBe 2OM1 · UniProt P01308
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