5E26 | pdb_00005e26

Crystal structure of human PANK2: the catalytic core domain in complex with pantothenate and adenosine diphosphate

PDB DOI: https://doi.org/10.2210/pdb5E26/pdb

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

Deposited: 2015-09-30 Released: 2015-10-21
Deposition Author(s): DONG, A., LOPPNAU, P., RAVICHANDRAN, M., CHENG, C., TEMPEL, W., SEITOVA, A., HUTCHINSON, A., HONG, B.S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.251 (Depositor), 0.249 (DCC)
R-Value Work:
0.214 (Depositor), 0.218 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human PANK2: the catalytic core domain in complex with pantothenate and adenosine diphosphate

LOPPNAU, P., DONG, A., RAVICHANDRAN, M., CHENG, C., TEMPEL, W., SEITOVA, A., HUTCHINSON, A., HONG, B.S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 165.93 kDa
Atom Count: 11,611
Modeled Residue Count: 1,443
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantothenate kinase 2, mitochondrial	A, B, C, D	365	Homo sapiens	Mutation(s): 0 Gene Names: PANK2, C20orf48 EC: 2.7.1.33
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZ23 (Homo sapiens) Explore Q9BZ23 Go to UniProtKB: Q9BZ23
PHAROS: Q9BZ23 GTEx: ENSG00000125779
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BZ23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain E [auth A]	E [auth A], L [auth B], P [auth C], T [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
PAU Query on PAU Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain K [auth B]	F [auth A], K [auth B], Q [auth C], S [auth D]	PANTOTHENOIC ACID C₉ H₁₇ N O₅ GHOKWGTUZJEAQD-ZETCQYMHSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain S [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain U [auth D] mmCIF format, chain G [auth A] mmCIF format, chain U [auth D]	G [auth A], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain U [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain V [auth D] MOL2 format, chain M [auth B] MOL2 format, chain V [auth D] mmCIF format, chain M [auth B] mmCIF format, chain V [auth D]	M [auth B], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Focus chain V [auth D] Interactions & Density Focus chain M [auth B] Focus chain V [auth D]
UNX Query on UNX 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 N [auth B] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain O [auth B]	H [auth A] I [auth A] J [auth A] N [auth B] O [auth B] H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], R [auth C], W [auth D], X [auth D], Y [auth D]	UNKNOWN ATOM OR ION X		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.251 (Depositor), 0.249 (DCC)
R-Value Work: 0.214 (Depositor), 0.218 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.874	α = 90
b = 109.717	β = 90
c = 142.571	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-10-21

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2015-10-21
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description