4K8K

Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with 1-(4-methoxyphenyl)-1-cyclopropane and 2-aminoperimidine

PDB DOI: https://doi.org/10.2210/pdb4K8K/pdb

Classification: TRANSFERASE
Organism(s): Rhizobium etli CFN 42
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-04-18 Released: 2013-05-01
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.218
R-Value Work: 0.181
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with 1-(4-methoxyphenyl)-1-cyclopropane and 2-aminoperimidine

Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 80.16 kDa
Atom Count: 6,042
Modelled Residue Count: 661
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sugar kinase	A, B	352	Rhizobium etli CFN 42	Mutation(s): 0 Gene Names: RHE_CH00135
UniProt
Find proteins for Q2KDX6 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2KDX6 Go to UniProtKB: Q2KDX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2KDX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADN Query on ADN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain L [auth B]	C [auth A], L [auth B]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B]
1PJ Query on 1PJ Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B]	D [auth A], M [auth B]	1-(4-methoxyphenyl)cyclopropanecarboxylic acid C₁₁ H₁₂ O₃ WCPFQQHADRJANG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B]
1PK Query on 1PK Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] J [auth B] E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], N [auth B], O [auth B]	1H-perimidin-2-amine C₁₁ H₉ N₃ UNDUSVBXIVZGOQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth B] Focus chain O [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B]	I [auth A], P [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.218
R-Value Work: 0.181
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.592	α = 90
b = 91.1	β = 90
c = 93.34	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-05-01

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-05-01
Type: Initial release
Version 1.1: 2013-05-08
Changes: Structure summary
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary