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
Deposition Author(s): Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 76.09 kDa
Atom Count: 5,645
Modelled Residue Count: 524
Deposited Residue Count: 531
Unique protein chains: 2
Unique nucleic acid chains: 1

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 Annotations Expand
Reference Sequence

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 Annotations Expand
Reference Sequence

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 Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	D [auth A]	2		N/A	Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1TU Query on 1TU Download Ideal Coordinates CCD File SDF format, chain G [auth R] MOL2 format, chain G [auth R]	G [auth R]	4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol C₁₂ H₁₂ F₂ N₂ O₂ MSZRPLCUVKFQJC-UHFFFAOYSA-N		Interactions Focus chain G [auth R] Interactions & Density Focus chain G [auth R]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth R] MOL2 format, chain E [auth R]	E [auth R]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth R] Interactions & Density Focus chain E [auth R]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth R] MOL2 format, chain F [auth R]	F [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]

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		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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 Package:

Software Name	Purpose
ADSC	data collection
RAPD	model building
PHENIX	refinement
HKL-2000	data reduction
RAPD	data scaling
RAPD	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-06-18

Deposition Author(s):

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