Download MendeleyIon binding properties of a naturally occurring metalloantibody
Farokhi, E., Fleming, J.K., Erasmus, M.F., Ward, A.D., Wu, Y., Gutierrez, M.G., Wojciak, J.M., Huxford, T.(2020) Antibodies (Basel) 9: 10
6VRT
LT1009 humanized antibody Fab fragment in complex with calcium
- PDB DOI: https://doi.org/10.2210/pdb6VRT/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Cricetulus griseus
- Mutation(s): No
- Deposited: 2020-02-09 Released: 2020-04-29
- Funding Organization(s): National Science Foundation (United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.56 Å
- R-Value Free: 0.260
- R-Value Work: 0.209
- R-Value Observed: 0.211
wwPDB Validation 3D Report Full Report
Currently 6VRT does not have a validation slider image.
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Sonepcizumab antibody Fab fragment, heavy chain | A [auth H] | 225 | 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: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Sonepcizumab antibody Fab fragment, light chain | B [auth L] | 214 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth H] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| CA Query on CA | D [auth L], E [auth L] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.56 Å
- R-Value Free: 0.260
- R-Value Work: 0.209
- R-Value Observed: 0.211
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 87.802 | α = 90 |
| b = 114.408 | β = 90 |
| c = 133.702 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
Structure Validation
Currently 6VRT does not have a validation slider image.
Entry History & Funding Information
Deposition Data
- Released Date: 2020-04-29 Deposition Author(s): Fleming, J.K., Huxford, T.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Science Foundation (United States) | United States | CHE-1112547 |
Revision History (Full details and data files)
- Version 1.0: 2020-04-29
Type: Initial release - Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
