4FR4 | pdb_00004fr4

Crystal structure of human serine/threonine-protein kinase 32A (YANK1)

PDB DOI: https://doi.org/10.2210/pdb4FR4/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2012-06-26 Released: 2012-07-18
Deposition Author(s): Chaikuad, A., Elkins, J.M., Krojer, T., Mahajan, P., Goubin, S., Szklarz, M., Tumber, A., Wang, J., Savitsky, P., Shrestha, B., Daga, N., Picaud, S., Fedorov, O., Allerston, C.K., Latwiel, S.V.A., Vollmar, M., Canning, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.244 (Depositor), 0.247 (DCC)
R-Value Work:
0.204 (Depositor), 0.207 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Models: experimental
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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 human serine/threonine-protein kinase 32A (YANK1)

Chaikuad, A., Elkins, J.M., Krojer, T., Mahajan, P., Goubin, S., Szklarz, M., Tumber, A., Wang, J., Savitsky, P., Shrestha, B., Daga, N., Picaud, S., Fedorov, O., Allerston, C.K., Latwiel, S.V.A., Vollmar, M., Canning, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 274.28 kDa
Atom Count: 18,277
Modeled Residue Count: 2,078
Deposited Residue Count: 2,304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 32A	A, B, C, D, E A, B, C, D, E, F	384	Homo sapiens	Mutation(s): 0 Gene Names: STK32A EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WU08 (Homo sapiens) Explore Q8WU08 Go to UniProtKB: Q8WU08
PHAROS: Q8WU08 GTEx: ENSG00000169302
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WU08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STU Query on STU Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F]	G [auth A] I [auth B] L [auth C] P [auth D] Q [auth E] G [auth A], I [auth B], L [auth C], P [auth D], Q [auth E], S [auth F]	STAUROSPORINE C₂₈ H₂₆ N₄ O₃ HKSZLNNOFSGOKW-FYTWVXJKSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth E] SDF format, chain T [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F]	H [auth A] J [auth B] K [auth B] M [auth C] N [auth C] H [auth A], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C], R [auth E], T [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth E] Focus chain T [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth E] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.244 (Depositor), 0.247 (DCC)
R-Value Work: 0.204 (Depositor), 0.207 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.11	α = 90
b = 154.11	β = 90
c = 112.11	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-07-18

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2012-07-18
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-27
Changes: Structure summary