Research workbench
Insulin receptor ectodomain construct comprising domains L1-cr in complex with high-affinity insulin analogue [D-pro-B26]-dti-NH2, alphact PEPTIDE(693-719) and Fab 83-7
Analyse Insulin receptor ectodomain construct comprising domains L1-cr in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W13
- Type
- protein
- Length
- 565 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin receptor domains L1-cr; Monoclonal antibody Fab 83-7 fragment - heavy chain…
- EC
- 2.7.10.1
- UniProt
- P06213, P01308
- Ligands
- NAG, BMA, MAN
- Pockets
- 7 · best druggability 0.49
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Insulin receptor domains L1-cr (EC 2.7.10.1) | protein | 288 | 11% helix, 33% strand | P06213 |
| C | Monoclonal antibody Fab 83-7 fragment - heavy chain | protein | 116 | 5% helix, 47% strand | — |
| D | Monoclonal antibody Fab 83-7 fragment - light chain | protein | 114 | 3% helix, 50% strand | — |
| A | Insulin a chain | protein | 21 | 57% helix, 0% strand | P01308 |
| B | Insulin B chain | protein | 15 | 80% helix, 0% strand | P01308 |
| F | Insulin receptor alphact peptide (EC 2.7.10.1) | protein | 11 | 64% helix, 0% strand | P06213 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains E, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.49 | 0.76 | 28 | empty |
| 2 | 101 | 0.47 | 0.80 | 21 | NAG |
| 3 | 109 | 0.41 | 0.76 | 23 | empty |
| 4 | 95 | 0.35 | 0.74 | 18 | empty |
| 5 | 71 | 0.33 | 0.76 | 20 | empty |
Interfaces
9 interfaces between chains.
- C–D · 944 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 515 Ų buried · 1 hydrogen bond · protein-protein
- E–C · 493 Ų buried · 7 hydrogen bonds · protein-protein
- E–D · 410 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 370 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3W13 · Insulin receptor ectodomain construct comprising domains L1-CR in complex with… · 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 E against A, TM-score 0.98
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 P06213
- Every structure of UniProt P01308
- Elsewhere: RCSB PDB 3W13 · PDBe 3W13 · UniProt P06213 · UniProt P01308
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