Research workbench
Head region of the open conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II.
Analyse Head region of the open conformation of the human type 1 insulin-like growth… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VWG
- Type
- protein
- Length
- 800 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain…
- EC
- 2.7.10.1
- UniProt
- P08069, P03069, P01344
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 18% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain (EC 2.7.10.1) | protein | 439 | 14% helix, 25% strand | P08069, P03069 |
| B | Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain (EC 2.7.10.1) | protein | 307 | 18% helix, 26% strand | P08069, P03069 |
| I | Insulin-like growth factor II | protein | 54 | 48% helix, 4% strand | P01344 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.79 | 0.81 | 79 | empty |
| 2 | 1135 | 0.73 | 0.77 | 86 | empty |
| 3 | 222 | 0.50 | 0.76 | 28 | empty |
| 4 | 168 | 0.50 | 0.78 | 32 | empty |
| 5 | 119 | 0.49 | 0.80 | 23 | NAG |
Interfaces
3 interfaces between chains.
- A–B · 1492 Ų buried · 10 hydrogen bonds · protein-protein
- B–I · 864 Ų buried · 6 hydrogen bonds · protein-protein
- A–I · 623 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6VWG · Head region of the open conformation of the human type 1 insulin-like growth factor… · the same entry in another collection · chain A against A, TM-score 1.00
- P01344 · AlphaFold monomer V2.0 prediction for insulin-like growth factor II (P01344) · a predicted model of the same protein · chain I against A, TM-score 0.66
- P03069 · AlphaFold monomer V2.0 prediction for general control transcription factor GCN4 (P03069) · a predicted model of the same protein · chain B against A, TM-score 0.17
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 P08069
- Every structure of UniProt P03069
- Every structure of UniProt P01344
- Elsewhere: RCSB PDB 6VWG · PDBe 6VWG · UniProt P08069 · UniProt P03069 · UniProt P01344
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