Research workbench
Leucine-zippered human insulin receptor ectodomain with single bound insulin - "upper" membrane-distal part
Analyse Leucine-zippered human insulin receptor ectodomain with single bound insulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HN5
- Type
- protein
- Length
- 953 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin; Insulin RECEPTOR,GENERAL control protein GCN4
- EC
- 2.7.10.1
- UniProt
- P01308, P06213, P03069
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 12% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin | protein | 21 | 52% helix, 0% strand | P01308 |
| B | Insulin | protein | 25 | 24% helix, 0% strand | P01308 |
| E | Insulin RECEPTOR,GENERAL control protein GCN4 (EC 2.7.10.1) | protein | 584 | 8% helix, 29% strand | P06213, P03069 |
| F | Insulin RECEPTOR,GENERAL control protein GCN4 (EC 2.7.10.1) | protein | 323 | 16% helix, 27% strand | P06213, P03069 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains E, A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.86 | 0.87 | 108 | empty |
| 2 | 1143 | 0.72 | 0.76 | 93 | empty |
| 3 | 406 | 0.64 | 0.78 | 36 | empty |
| 4 | 223 | 0.49 | 0.75 | 30 | empty |
| 5 | 121 | 0.48 | 0.80 | 16 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1801 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 620 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 531 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 477 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 364 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6HN5 · Leucine-zippered human insulin receptor ectodomain with single bound insulin - "upper"… · the same entry in another collection · chain F against F, TM-score 1.00
- P06213 · AlphaFold monomer V2.0 prediction for insulin receptor (P06213) · a predicted model of the same protein · chain F against A, TM-score 0.82
- P03069 · AlphaFold monomer V2.0 prediction for general control transcription factor GCN4 (P03069) · a predicted model of the same protein · chain F against A, TM-score 0.18
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
- Every structure of UniProt P06213
- Every structure of UniProt P03069
- Elsewhere: RCSB PDB 6HN5 · PDBe 6HN5 · UniProt P01308 · UniProt P06213 · UniProt P03069
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