4KZD
Crystal structure of an RNA aptamer in complex with fluorophore and Fab
- PDB DOI: https://doi.org/10.2210/pdb4KZD/pdb
- NAKB: 4KZD
- Classification: immune system/rna
- Organism(s): Mus musculus
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2013-05-29 Released: 2014-06-18 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.19 Å
- R-Value Free: 0.211 
- R-Value Work: 0.179 
- R-Value Observed: 0.180 
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 |
BL3-6 Fab antibody, heavy chain | A [auth H] | 232 | 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 |
BL3-6 Fab antibody, light chain | B [auth L] | 215 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
RNA (84-MER) | C [auth R] | 84 | N/A | ||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
1TU Query on 1TU | G [auth R] | 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol C12 H12 F2 N2 O2 MSZRPLCUVKFQJC-UHFFFAOYSA-N | |||
K Query on K | E [auth R] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
MG Query on MG | F [auth R] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900003 Query on PRD_900003 | D [auth A] | sucrose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.19 Å
- R-Value Free: 0.211 
- R-Value Work: 0.179 
- R-Value Observed: 0.180 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 148.425 | α = 90 |
b = 79.602 | β = 111.65 |
c = 95.21 | γ = 90 |
Software Name | Purpose |
---|---|
ADSC | data collection |
RAPD | model building |
PHENIX | refinement |
HKL-2000 | data reduction |
RAPD | data scaling |
RAPD | phasing |
Entry History 
Deposition Data
- Released Date: 2014-06-18  Deposition Author(s): Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.
Revision History (Full details and data files)
- Version 1.0: 2014-06-18
Type: Initial release - Version 1.1: 2014-07-09
Changes: Database references - Version 1.2: 2014-07-30
Changes: Database references - Version 1.3: 2015-05-20
Changes: Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary