4IXD | pdb_00004ixd

X-ray structure of lfa-1 i-domain in complex with ibe-667 at 1.8a resolution

PDB DOI: https://doi.org/10.2210/pdb4IXD/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-01-25 Released: 2014-01-29
Deposition Author(s): Kallen, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.199 (Depositor), 0.195 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4IXD

Ligand Structure Quality Assessment

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

Literature

Identification and x-ray structure based investigation of an ICAM-1 binding enhancing small molecule activator of LFA-1

Hintersteiner, M., Kallen, J., Schmied, M., Jung, T., Graf, C., Mudd, G., Gstach, H., Auer, M.

To be published.

Macromolecule Content

Total Structure Weight: 21.88 kDa
Atom Count: 1,815
Modeled Residue Count: 182
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-L	A	188	Homo sapiens	Mutation(s): 0 Gene Names: ITGAL, CD11A
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens) Explore P20701 Go to UniProtKB: P20701
PHAROS: P20701 GTEx: ENSG00000005844
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20701
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1HV Query on 1HV Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-(3-{4-[(3-aminopropyl)carbamoyl]phenyl}-1H-indazol-1-yl)-N-methylbenzamide C₂₅ H₂₅ N₅ O₂ CGHZINICBUGRGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.80 Å
R-Value Free: 0.199 (Depositor), 0.195 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.3	α = 90
b = 65.9	β = 90
c = 133.6	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
X-PLOR	model building
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-01-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-29
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.