5TVT | pdb_00005tvt

Structure of Maternal Embryonic Leucine Zipper Kinase

PDB DOI: https://doi.org/10.2210/pdb5TVT/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-11-10 Released: 2017-11-15
Deposition Author(s): Seo, H.-Y., Huang, H., Gray, N.S., Dhe-Paganon, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.229 (Depositor), 0.234 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)
R-Value Observed:
0.192 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of Maternal Embryonic Leucine Zipper Kinase

Seo, H.-Y., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 39.21 kDa
Atom Count: 2,667
Modeled Residue Count: 321
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maternal embryonic leucine zipper kinase	A	334	Homo sapiens	Mutation(s): 0 Gene Names: MELK, KIAA0175 EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14680 (Homo sapiens) Explore Q14680 Go to UniProtKB: Q14680
PHAROS: Q14680 GTEx: ENSG00000165304
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14680
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7LV Query on 7LV 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]	9-(3,5-dichloro-4-hydroxyphenyl)-1-{trans-4-[(dimethylamino)methyl]cyclohexyl}-3-methyl-3,4-dihydropyrimido[5,4-c][1,5]naphthyridin-2(1H)-one C₂₆ H₂₉ Cl₂ N₅ O₂ HHDFQGMZNYJMHI-RZDIXWSQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.229 (Depositor), 0.234 (DCC)
R-Value Work: 0.190 (Depositor), 0.192 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.69	α = 90
b = 68.65	β = 90
c = 105.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

Dhe-Paganon, S.

Revision History (Full details and data files)

Version 1.0: 2017-11-15
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.