5R63 | pdb_00005r63

PanDDA analysis group deposition -- Crystal Structure of FIBRINOGEN-LIKE GLOBE DOMAIN OF HUMAN TENASCIN-C in complex with Z319545618

PDB DOI: https://doi.org/10.2210/pdb5R63/pdb
Deposition Group: G_1002131 (changed state) | Explore G_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: 1.59 Å
R-Value Free:
0.220 (Depositor), 0.225 (DCC)
R-Value Work:
0.180 (Depositor), 0.188 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 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: 25.38 kDa
Atom Count: 1,876
Modeled Residue Count: 211
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24821
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RXS Query on RXS 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]	3-[(2-methyl-1H-imidazol-1-yl)methyl]benzonitrile C₁₂ H₁₁ N₃ HMXUYPBDUYSWMA-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: 1.59 Å
R-Value Free: 0.220 (Depositor), 0.225 (DCC)
R-Value Work: 0.180 (Depositor), 0.188 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.35	α = 90
b = 77.35	β = 90
c = 71.8	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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: Advisory, Data collection, Database references, Structure summary
Version 1.2: 2026-02-18
Changes: Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.