2UYY

Structure of the cytokine-like nuclear factor n-pac

PDB DOI: https://doi.org/10.2210/pdb2UYY/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-04-20 Released: 2007-07-03
Deposition Author(s): Tickle, J., Pilka, E.S., Bunkoczi, G., Berridge, G., Smee, C., Kavanagh, K.L., Hozjan, V., Niesen, F.H., Papagrigoriou, E., Pike, A.C.W., Turnbull, A., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Weigelt, J., von Delft, F., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.211
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The Structure of the Cytokine-Like Nuclear Factor N-Pac

Tickle, J., Pilka, E.S., Bunkoczi, G., Berridge, G., Smee, C., Kavanagh, K.L., Hozjan, V., Niesen, F.H., Papagrigoriou, E., Pike, A.C.W., Turnbull, A., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Weigelt, J., von Delft, F., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 137.75 kDa
Atom Count: 9,183
Modelled Residue Count: 1,167
Deposited Residue Count: 1,264
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-PAC PROTEIN	A, B, C, D	316	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q49A26 (Homo sapiens) Explore Q49A26 Go to UniProtKB: Q49A26
PHAROS: Q49A26 GTEx: ENSG00000140632
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q49A26
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA7 Query on NA7 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth D]	F [auth A], J [auth D]	[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE C₁₅ H₂₄ N₅ O₁₆ P₃ XDDBFIXGEVGCEU-AOOZFPJJSA-N		Interactions Focus chain F [auth A] Focus chain J [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D]	E [auth A], G [auth B], H [auth C], I [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.211
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.18	α = 90
b = 134.18	β = 90
c = 261.463	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-07-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-07-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2018-02-28
Changes: Source and taxonomy
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

Prepare Data

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Deposit Data

Help and Resources

2UYY

Structure of the cytokine-like nuclear factor n-pac

The Structure of the Cytokine-Like Nuclear Factor N-Pac

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)