4DB5 | pdb_00004db5

Crystal structure of Rabbit GITRL

PDB DOI: https://doi.org/10.2210/pdb4DB5/pdb

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

Deposited: 2012-01-13 Released: 2012-03-21
Deposition Author(s): Kumar, P.R., Bhosle, R., Gizzi, A., Scott Glenn, A., Chowhury, S., Hillerich, B., Seidel, 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: 1.52 Å
R-Value Free:
0.176 (Depositor), 0.174 (DCC)
R-Value Work:
0.161 (Depositor), 0.159 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of GITRL from Oryctolagus cuniculus

Kumar, P.R., Bhosle, R., Gizzi, A., Scott Glenn, A., Chowhury, S., Hillerich, B., Seidel, R., Nathenson, S.G., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 14.34 kDa
Atom Count: 1,181
Modeled Residue Count: 121
Deposited Residue Count: 125
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 18	A	125	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: GITRL, TNFSF18
UniProt
Find proteins for G1TIM1 (Oryctolagus cuniculus) Explore G1TIM1 Go to UniProtKB: G1TIM1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TIM1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P 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]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-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: 1.52 Å
R-Value Free: 0.176 (Depositor), 0.174 (DCC)
R-Value Work: 0.161 (Depositor), 0.159 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.047	α = 90
b = 127.047	β = 90
c = 127.047	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

Scott Glenn, A.

Nathenson, S.G.

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: 2012-06-06
Changes: Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

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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.