4U40 | pdb_00004u40

Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) Bound to AMPPNP

PDB DOI: https://doi.org/10.2210/pdb4U40/pdb

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

Deposited: 2014-07-23 Released: 2016-01-06
Deposition Author(s): Harris, S.F., Wu, P., Coons, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.262 (Depositor), 0.256 (DCC)
R-Value Work:
0.198 (Depositor), 0.193 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4U40

Ligand Structure Quality Assessment

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

Literature

Structural Plasticity and Kinase Activation in a Cohort of MAP4K4 Structures

Wu, P., Chen, H., Coons, M., Crawford, T.D., Kirkpatrick, D.S., Murray, L., Ndubaku, C.O., Nonomiya, J., Pham, V., Schmidt, S., Smysczek, T., Vitorino, P., Ye, W., Harris, S.F.

To be published.

Macromolecule Content

Total Structure Weight: 76.32 kDa
Atom Count: 4,991
Modeled Residue Count: 594
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase kinase 4	A, B	332	Homo sapiens	Mutation(s): 0 Gene Names: MAP4K4, HGK, KIAA0687, NIK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O95819 (Homo sapiens) Explore O95819 Go to UniProtKB: O95819
PHAROS: O95819 GTEx: ENSG00000071054
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95819
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.262 (Depositor), 0.256 (DCC)
R-Value Work: 0.198 (Depositor), 0.193 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.339	α = 90
b = 87.595	β = 90
c = 91.45	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-01-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-06
Type: Initial release
Version 1.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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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.