3KEU | pdb_00003keu

Crystal Structure of Human PL Kinase with bound PLP and ATP

PDB DOI: https://doi.org/10.2210/pdb3KEU/pdb

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

Deposited: 2009-10-26 Released: 2009-11-03
Deposition Author(s): Safo, M.K., Gandhi, A.K., Musayev, F.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.256 (Depositor), 0.241 (DCC)
R-Value Work:
0.209 (Depositor), 0.195 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme

Gandhi, A.K., Musayev, F.N., Safo, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 73.77 kDa
Atom Count: 5,357
Modeled Residue Count: 610
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal kinase	A, B	312	Homo sapiens	Mutation(s): 0 Gene Names: C21orf124, C21orf97, PDXK, PKH, PNK EC: 2.7.1.35
UniProt & NIH Common Fund Data Resources
Find proteins for O00764 (Homo sapiens) Explore O00764 Go to UniProtKB: O00764
PHAROS: O00764 GTEx: ENSG00000160209
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00764
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth B]	F [auth A], Q [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain Q [auth B]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain G [auth A] MOL2 format, chain S [auth B] MOL2 format, chain G [auth A] mmCIF format, chain S [auth B] mmCIF format, chain G [auth A]	G [auth A], S [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain S [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain U [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain T [auth B] SDF format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain T [auth B] mmCIF format, chain R [auth B]	H [auth A] I [auth A] J [auth A] R [auth B] T [auth B] H [auth A], I [auth A], J [auth A], R [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain CA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain CA [auth B]	AA [auth B] BA [auth B] CA [auth B] K [auth A] L [auth A] AA [auth B], BA [auth B], CA [auth B], K [auth A], L [auth A], M [auth A], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	C [auth A], D [auth A], N [auth B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain N [auth B] Focus chain O [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B]	E [auth A], P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.256 (Depositor), 0.241 (DCC)
R-Value Work: 0.209 (Depositor), 0.195 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.202	α = 90
b = 114.585	β = 90
c = 169.414	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-11-03

Deposition Author(s):

Safo, M.K.

Gandhi, A.K.

Musayev, F.N.

Revision History (Full details and data files)

Version 1.0: 2009-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations