6ANH

Crystal structure of PPK2 class III in complex with Guanosine 5-tetraphosphate

PDB DOI: https://doi.org/10.2210/pdb6ANH/pdb

Classification: TRANSFERASE
Organism(s): Cytophaga hutchinsonii ATCC 33406
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-13 Released: 2019-01-16
Deposition Author(s): Nocek, B., Joachimiak, A., Yakunin, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.238
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases

Nocek, B., Khusnutdinova, A.N., Ruszkowski, M., Flick, R., Burda, M., Batyrova, K., Brown, G., Mucha, A., Joachimiak, A., Berlicki, L., Yakunin, A.F.

(2018) ACS Catal 8: 10746-10760

DOI: https://doi.org/10.1021/acscatal.8b03151

Macromolecule Content

Total Structure Weight: 36.14 kDa
Atom Count: 2,423
Modelled Residue Count: 300
Deposited Residue Count: 305
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyphosphate:AMP phosphotransferase	A	305	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0 Gene Names: CHU_0107 EC: 2.7.4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BKP Query on BKP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	5'-O-[(S)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine C₁₀ H₁₇ N₅ O₁₇ P₄ KDFXXNGTULMGMF-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.238
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.812	α = 90
b = 110.812	β = 90
c = 178.807	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-01-16
Type: Initial release
Version 1.1: 2020-07-29
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.