5R5T | pdb_00005r5t

PanDDA analysis group deposition -- Crystal Structure of FIBRINOGEN-LIKE GLOBE DOMAIN OF HUMAN TENASCIN-C in complex with Z1251207602

PDB DOI: https://doi.org/10.2210/pdb5R5T/pdb
Deposition Group: G_1002131 (changed state) ExploreG_1002131

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-28 Released: 2020-10-28
Deposition Author(s): Coker, J.A., Bezerra, G.A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Yue, W.W., Marsden, B.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.215 (Depositor), 0.220 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

PanDDA analysis group deposition

Coker, J.A., Bezerra, G.A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Yue, W.W., Marsden, B.D.

To be published.

Macromolecule Content

Total Structure Weight: 25.37 kDa
Atom Count: 1,866
Modeled Residue Count: 211
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tenascin C (Hexabrachion), isoform CRA_a	A	220	Homo sapiens	Mutation(s): 0 Gene Names: TNC, hCG_29852
UniProt & NIH Common Fund Data Resources
Find proteins for P24821 (Homo sapiens) Explore P24821 Go to UniProtKB: P24821
PHAROS: P24821 GTEx: ENSG00000041982
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24821
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RWS Query on RWS Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-(5-methyl-1,3,4-thiadiazol-2-yl)piperidine C₈ H₁₃ N₃ S IIDJDXATFNHHGO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.215 (Depositor), 0.220 (DCC)
R-Value Work: 0.179 (Depositor), 0.190 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.46	α = 90
b = 77.46	β = 90
c = 71.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-10-28

Deposition Author(s):

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2020-10-28
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.