4E4S

Crystal structure of Pika GITRL

PDB DOI: https://doi.org/10.2210/pdb4E4S/pdb

Classification: IMMUNE SYSTEM
Organism(s): Ochotona princeps
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-13 Released: 2012-03-21
Deposition Author(s): Kumar, P.R., Bhosle, R., Bonanno, J., Chowdhury, S., Gizzi, A., Glen, S., Hillerich, B., Hammonds, J., Seidel, R., Toro, R., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.178 (Depositor), 0.180 (DCC)
R-Value Work:
0.147 (Depositor), 0.150 (DCC)
R-Value Observed:
0.148 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of GITRL from Ochotona princeps

Kumar, P.R., Bhosle, R., Bonanno, J., Chowdhury, S., Gizzi, A., Glen, S., Hillerich, B., Hammonds, J., Seidel, R., Toro, R., Nathenson, S.G., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 84.64 kDa
Atom Count: 5,747
Modelled Residue Count: 687
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 18	A, B, C, D, E A, B, C, D, E, F	125	Ochotona princeps	Mutation(s): 0 Gene Names: GITRL
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain M [auth E] SDF format, chain N [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F]	G [auth A] H [auth B] I [auth C] J [auth C] K [auth D] G [auth A], H [auth B], I [auth C], J [auth C], K [auth D], L [auth E], M [auth E], N [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth F] MOL2 format, chain O [auth F] mmCIF format, chain O [auth F]	O [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth F] Interactions & Density Focus chain O [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.178 (Depositor), 0.180 (DCC)
R-Value Work: 0.147 (Depositor), 0.150 (DCC)
R-Value Observed: 0.148 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.371	α = 90
b = 164.588	β = 117.16
c = 54.103	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Atoms-to-Animals: The Immune Function Network (IFN)

Revision History (Full details and data files)

Version 1.0: 2012-03-21
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary