6VKJ | pdb_00006vkj

Crystal structure of the G domain of human guanylate-binding protein 2 (hGBP2) in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb6VKJ/pdb

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

Deposited: 2020-01-21 Released: 2021-01-27
Deposition Author(s): Roy, S., Wang, B., Tian, Y., Yin, Q.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.226 (Depositor)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the G domain of human guanylate-binding protein 2 (hGBP2) in complex with GDP

Roy, S., Wang, B., Tian, Y., Yin, Q.

To be published.

Macromolecule Content

Total Structure Weight: 34.45 kDa
Atom Count: 2,552
Modeled Residue Count: 305
Deposited Residue Count: 305
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate-binding protein 2	A	305	Homo sapiens	Mutation(s): 0 Gene Names: GBP2 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P32456 (Homo sapiens) Explore P32456 Go to UniProtKB: P32456
PHAROS: P32456 GTEx: ENSG00000162645
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32456
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP 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]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.226 (Depositor)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.184 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.951	α = 90
b = 87.951	β = 90
c = 105.279	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R00AI108793

Revision History (Full details and data files)

Version 1.0: 2021-01-27
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, 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.