MolNFT v1 · #122904 · protein
Human insulin receptor domains L1-cr in complex with peptide S519C16 and 83-7 fv
5J3H: “Human insulin receptor domains L1-cr in complex with peptide S519C16 and 83-7 fv”. X-ray diffraction, 4 ligands (NAG, FUC, MAN), 8 pockets (best druggability 0.47). MolNFT v1 #122904 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5J3H
- Type
- protein
- Length
- 513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide S519C16; Mab 83-7 Fab heavy chain; Mab 83-7 Fab light chain; Insulin receptor
- EC
- 2.7.10.1
- UniProt
- P06213
- Ligands
- NAG, FUC, MAN, BMA
- Pockets
- 8 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Peptide S519C16 | protein | 14 | 79% helix, 0% strand | — |
| C | Mab 83-7 Fab heavy chain | protein | 116 | 8% helix, 47% strand | — |
| D | Mab 83-7 Fab light chain | protein | 112 | 3% helix, 52% strand | — |
| E | Insulin receptor (EC 2.7.10.1) | protein | 271 | 9% helix, 32% strand | P06213 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains E, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains E
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.47 | 0.76 | 30 | empty |
| 2 | 89 | 0.47 | 0.81 | 21 | empty |
| 3 | 148 | 0.45 | 0.77 | 28 | empty |
| 4 | 74 | 0.37 | 0.77 | 15 | empty |
| 5 | 53 | 0.36 | 0.79 | 13 | empty |
Interfaces
4 interfaces between chains.
- C–D · 927 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 583 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 496 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 395 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5J3H · Human insulin receptor domains L1-CR in complex with peptide S519C16 and 83-7 Fv · the same entry in another collection · chain B against B, 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 0.99
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
- Elsewhere: RCSB PDB 5J3H · PDBe 5J3H · UniProt P06213
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