2Y7J

Structure of human phosphorylase kinase, gamma 2

PDB DOI: https://doi.org/10.2210/pdb2Y7J/pdb

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

Deposited: 2011-01-31 Released: 2011-02-09
Deposition Author(s): Muniz, J.R.C., Shrestha, A., Savitsky, P., Wang, J., Rellos, P., Fedorov, O., Burgess-Brown, N., Brenner, B., Berridge, G., Elkins, J.M., Krojer, T., Vollmar, M., Che, K.H., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.216 (Depositor), 0.230 (DCC)
R-Value Work:
0.182 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of Human Phosphorylase Kinase, Gamma 2

Muniz, J.R.C., Shrestha, A., Savitsky, P., Wang, J., Rellos, P., Fedorov, O., Burgess-Brown, N., Brenner, B., Berridge, G., Elkins, J.M., Krojer, T., Vollmar, M., Che, K.H., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 171.27 kDa
Atom Count: 9,378
Modelled Residue Count: 1,130
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORYLASE B KINASE GAMMA CATALYTIC CHAIN, TESTIS/LIVER ISOFORM	A, B, C, D	365	Homo sapiens	Mutation(s): 0 EC: 2.7.11.19
UniProt & NIH Common Fund Data Resources
Find proteins for P15735 (Homo sapiens) Explore P15735 Go to UniProtKB: P15735
PHAROS: P15735 GTEx: ENSG00000156873
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15735
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B49 Query on B49 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide C₂₂ H₂₇ F N₄ O₂ WINHZLLDWRZWRT-ATVHPVEESA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
B49	BindingDB: 2Y7J	Kd: min: 5.9, max: 39 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.216 (Depositor), 0.230 (DCC)
R-Value Work: 0.182 (Depositor), 0.190 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.79	α = 90
b = 91.42	β = 90
c = 164.48	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-02-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-02-09
Type: Initial release
Version 1.1: 2011-10-12
Changes: Atomic model, Data collection, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other, Structure summary