3W13
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
- PDB DOI: https://doi.org/10.2210/pdb3W13/pdb
- Classification: HORMONE RECEPTOR/HORMONE/IMMUNE SYSTEM
- Organism(s): Homo sapiens, Mus musculus
- Expression System: Cricetulus griseus, Mus musculus
- Mutation(s): No
- Deposited: 2012-11-06 Released: 2013-01-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 4.30 Å
- R-Value Free: 0.335
- R-Value Work: 0.289
- R-Value Observed: 0.291
This is version 2.1 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Insulin receptor domains L1-CR | A [auth E] | 310 | Homo sapiens | Mutation(s): 0 Gene Names: INSR EC: 2.7.10.1 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06213 (Homo sapiens) Explore P06213 Go to UniProtKB: P06213 | |||||
PHAROS: P06213 GTEx: ENSG00000171105 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06213 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| monoclonal antibody fab 83-7 fragment - heavy chain | B [auth C] | 116 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| monoclonal antibody fab 83-7 fragment - light chain | C [auth D] | 114 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Insulin A chain | D [auth A] | 21 | Homo sapiens | Mutation(s): 0 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01308 (Homo sapiens) Explore P01308 Go to UniProtKB: P01308 | |||||
PHAROS: P01308 GTEx: ENSG00000254647 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01308 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Insulin B chain | E [auth B] | 26 | Homo sapiens | Mutation(s): 0 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01308 (Homo sapiens) Explore P01308 Go to UniProtKB: P01308 | |||||
PHAROS: P01308 GTEx: ENSG00000254647 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01308 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Insulin receptor alphact peptide | 23 | Homo sapiens | Mutation(s): 0 EC: 2.7.10.1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06213 (Homo sapiens) Explore P06213 Go to UniProtKB: P06213 | |||||
PHAROS: P06213 GTEx: ENSG00000171105 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06213 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G | 4 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | I [auth E], J [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PR9 Query on PR9 | E [auth B] | D-PEPTIDE LINKING | C5 H10 N2 O |  | PRO |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 4.30 Å
- R-Value Free: 0.335
- R-Value Work: 0.289
- R-Value Observed: 0.291
- Space Group: P 2 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 169.228 | α = 90 |
| b = 169.228 | β = 90 |
| c = 169.228 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALA | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2013-01-09 Deposition Author(s): Lawrence, M.C., Smith, B.J., Brzozowski, A.M.
Revision History (Full details and data files)
- Version 1.0: 2013-01-09
Type: Initial release - Version 1.1: 2013-01-16
Changes: Database references - Version 1.2: 2013-09-04
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
