7SLZ

CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH BPF023596

PDB DOI: https://doi.org/10.2210/pdb7SLZ/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-25 Released: 2022-01-19
Deposition Author(s): Song, X., Dong, A., Calabrese, M., Wang, F., Owen, D., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.246
R-Value Work: 0.206
R-Value Observed: 0.208

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH BPF023596

Song, X., Dong, A., Calabrese, M., Wang, F., Owen, D., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 20.01 kDa
Atom Count: 1,339
Modelled Residue Count: 159
Deposited Residue Count: 167
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-induced degradation protein 4 homolog	A	167	Homo sapiens	Mutation(s): 0 Gene Names: GID4, C17orf39, VID24
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVV7 (Homo sapiens) Explore Q8IVV7 Go to UniProtKB: Q8IVV7
PHAROS: Q8IVV7 GTEx: ENSG00000141034
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IVV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9QU (Subject of Investigation/LOI) Query on 9QU 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]	N-[(1s,4s)-4-(1H-benzimidazol-2-yl)cyclohexyl]-N~2~-[(1H-indol-2-yl)methyl]glycinamide C₂₄ H₂₇ N₅ O HLHNFJNSQZZUNW-MAEOIBBWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
9QU	BindingDB: 7SLZ	Kd: 80 (nM) from 1 assay(s)
9QU	BindingDB: 7SLZ	IC50: 4100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.246
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: P 4₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M37SLZ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.264	α = 90
b = 40.264	β = 90
c = 202.958	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-01-19

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Other private	Canada	--

Revision History (Full details and data files)

Version 1.0: 2022-01-19
Type: Initial release
Version 1.1: 2022-03-16
Changes: Database references, Structure summary
Version 1.2: 2023-10-18
Changes: Data collection, Refinement description

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.