6SU9 | pdb_00006su9

Crystal structure of Plasmodium falciparum PdxK with ligands AMP-PNP and PL

PDB DOI: https://doi.org/10.2210/pdb6SU9/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-13 Released: 2019-10-23
Deposition Author(s): Groves, M.R., Gao, K., Wang, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.272 (Depositor), 0.283 (DCC)
R-Value Work:
0.209 (Depositor), 0.221 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

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 Plasmodium falciparum PdxK with ligands AMP-PNP and PL.

Gao, K., Wang, W., Groves, M.R.

(2019) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst9100534

Macromolecule Content

Total Structure Weight: 115.98 kDa
Atom Count: 4,885
Modeled Residue Count: 587
Deposited Residue Count: 994
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal kinase	A, B	497	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF3D7_0616000 EC: 2.7.1.35
UniProt
Find proteins for C6KT01 (Plasmodium falciparum (isolate 3D7)) Explore C6KT01 Go to UniProtKB: C6KT01
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6KT01
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
PXL Query on PXL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE C₈ H₉ N O₃ RADKZDMFGJYCBB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.272 (Depositor), 0.283 (DCC)
R-Value Work: 0.209 (Depositor), 0.221 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.703	α = 90
b = 62.004	β = 94.99
c = 93.712	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-10-23

Deposition Author(s):

Groves, M.R.

Gao, K.

Wang, W.

Revision History (Full details and data files)

Version 1.0: 2019-10-23
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description

6SU9 | pdb_00006su9

Crystal structure of Plasmodium falciparum PdxK with ligands AMP-PNP and PL

Literature

Crystal structure of Plasmodium falciparum PdxK with ligands AMP-PNP and PL.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand