2X18 | pdb_00002x18

The crystal structure of the PH domain of human AKT3 protein kinase

PDB DOI: https://doi.org/10.2210/pdb2X18/pdb

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

Deposited: 2009-12-22 Released: 2010-03-16
Deposition Author(s): Vollmar, M., Wang, J., Zhang, Y., Elkins, J.M., Burgess-Brown, N., Chaikuad, A., Pike, A.C.W., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.234 (Depositor), 0.244 (DCC)
R-Value Work:
0.189 (Depositor), 0.198 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structure of the Ph Domain of Human Akt3 Protein Kinase

Vollmar, M., Wang, J., Zhang, Y., Elkins, J.M., Burgess-Brown, N., Chaikuad, A., Pike, A.C.W., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 115.26 kDa
Atom Count: 9,414
Modeled Residue Count: 913
Deposited Residue Count: 952
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE	A, B, C, D, E A, B, C, D, E, F, G, H	119	Homo sapiens	Mutation(s): 0 EC: 2.7.11.1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y243 (Homo sapiens) Explore Q9Y243 Go to UniProtKB: Q9Y243
PHAROS: Q9Y243 GTEx: ENSG00000117020
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y243
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain L [auth H] SDF format, chain K [auth F] SDF format, chain J [auth E] SDF format, chain I [auth A] MOL2 format, chain L [auth H] MOL2 format, chain K [auth F] MOL2 format, chain J [auth E] MOL2 format, chain I [auth A] mmCIF format, chain L [auth H] mmCIF format, chain K [auth F] mmCIF format, chain J [auth E] mmCIF format, chain I [auth A]	I [auth A], J [auth E], K [auth F], L [auth H]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth E] Focus chain K [auth F] Focus chain L [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth E] Focus chain K [auth F] Focus chain L [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.234 (Depositor), 0.244 (DCC)
R-Value Work: 0.189 (Depositor), 0.198 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.475	α = 111.47
b = 62.401	β = 102.75
c = 71.411	γ = 94.36

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description