6FRJ
Crystal structure of scFv-SM3 in complex with APD-SeThrGalNAc-RP
- PDB DOI: https://doi.org/10.2210/pdb6FRJ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, synthetic construct
- Expression System: Komagataella pastoris
- Mutation(s): No
- Deposited: 2018-02-16 Released: 2019-02-20
- Funding Organization(s): MICINN
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.230
- R-Value Work: 0.205
- R-Value Observed: 0.206
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 |
| scFv-SM3 | A [auth H] | 244 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| APD-SeThr-RP | 7 | synthetic construct | Mutation(s): 0 |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A2G Query on A2G | G [auth B] | 2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N |  | ||
| EDO Query on EDO | C [auth H], D [auth H], E [auth H], F [auth H] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| T9E Query on T9E | B | L-PEPTIDE LINKING | C4 H9 N O2 Se |  | THR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.230
- R-Value Work: 0.205
- R-Value Observed: 0.206
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 35.353 | α = 90 |
| b = 68.612 | β = 90 |
| c = 90.609 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-02-20 Deposition Author(s): Companon, I., Castro-Lopez, J., Escudero-Casao, M., Avenoza, A., Busto, J.H., Castillon, S., Jimenez-Barbero, J., Bernardes, G.J., Boutureira, O., Jimenez-Oses, G., Asensio, J.L., Peregrina, J.M., Hurtado-Guerrero, R., Corzana, F.
| Funding Organization | Location | Grant Number |
|---|---|---|
| MICINN | Spain | CTQ2013-44367-C2-2-P |
| MICINN | Spain | BFU2016-75633-P |
Revision History (Full details and data files)
- Version 1.0: 2019-02-20
Type: Initial release - Version 1.1: 2019-03-06
Changes: Advisory, Data collection, Derived calculations - Version 1.2: 2019-03-13
Changes: Data collection, 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: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
