6O39
Crystal structure of Frizzled 5 CRD in complex with F2.I Fab
- PDB DOI: https://doi.org/10.2210/pdb6O39/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2019-02-26 Released: 2019-04-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.234
- R-Value Work: 0.196
- R-Value Observed: 0.198
wwPDB Validation 3D Report Full Report
Currently 6O39 does not have a validation slider image.
This is version 1.3 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 |
| Antibody F2.I Fab, Light chain | 213 | Homo sapiens | 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: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Antibody F2.I Fab, Heavy chain | 221 | Homo sapiens | 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 |
| Frizzled-5 | 123 | Homo sapiens | Mutation(s): 0 Gene Names: FZD5, C2orf31 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q13467 (Homo sapiens) Explore Q13467 Go to UniProtKB: Q13467 | |||||
PHAROS: Q13467 GTEx: ENSG00000163251 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q13467 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | Q [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| EDO Query on EDO | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | J [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.234
- R-Value Work: 0.196
- R-Value Observed: 0.198
- Space Group: P 61 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 101.405 | α = 90 |
| b = 101.405 | β = 90 |
| c = 196.497 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XPREP | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Structure Validation
Currently 6O39 does not have a validation slider image.
Entry History
Deposition Data
- Released Date: 2019-04-03 Deposition Author(s): Raman, S., Beilschmidt, M., Fransson, J., Julien, J.P.
Revision History (Full details and data files)
- Version 1.0: 2019-04-03
Type: Initial release - Version 1.1: 2019-04-17
Changes: Data collection, Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-10-11
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
