3DJC

CRYSTAL STRUCTURE OF PANTOTHENATE KINASE FROM LEGIONELLA PNEUMOPHILA

PDB DOI: https://doi.org/10.2210/pdb3DJC/pdb

Classification: TRANSFERASE
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Mutation(s): No

Deposited: 2008-06-23 Released: 2008-07-15
Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Romero, R., Dickey, M., Logan, C., Wasserman, S., Maletic, M., Koss, J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.313 (Depositor), 0.310 (DCC)
R-Value Work:
0.259 (Depositor), 0.260 (DCC)
R-Value Observed:
0.261 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Pantothenate Kinase from Legionella Pneumophila

Patskovsky, Y., Bonanno, J.B., Romero, R., Dickey, M., Logan, C., Maletic, M., Wasserman, S., Koss, J., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 348.91 kDa
Atom Count: 23,826
Modelled Residue Count: 3,040
Deposited Residue Count: 3,192
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III pantothenate kinase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	266	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: coaX, lpg0911 EC: 2.7.1.33
UniProt
Find proteins for Q5ZX22 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZX22 Go to UniProtKB: Q5ZX22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZX22
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain T [auth H] SDF format, chain U [auth H] SDF format, chain V [auth J] SDF format, chain W [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth H] MOL2 format, chain U [auth H] MOL2 format, chain V [auth J] MOL2 format, chain W [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth H] mmCIF format, chain U [auth H] mmCIF format, chain V [auth J] mmCIF format, chain W [auth L]	M [auth A] N [auth A] O [auth B] P [auth C] Q [auth C] M [auth A], N [auth A], O [auth B], P [auth C], Q [auth C], R [auth E], S [auth E], T [auth H], U [auth H], V [auth J], W [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth J] Focus chain W [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth J] Focus chain W [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.313 (Depositor), 0.310 (DCC)
R-Value Work: 0.259 (Depositor), 0.260 (DCC)
R-Value Observed: 0.261 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.394	α = 90
b = 134.571	β = 93.24
c = 134.404	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-07-15

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-07-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2012-10-24
Changes: Structure summary
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references