6CIA | pdb_00006cia

Crystal structure of aldo-keto reductase from Klebsiella pneumoniae in complex with NADPH.

PDB DOI: https://doi.org/10.2210/pdb6CIA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-02-23 Released: 2018-03-07
Deposition Author(s): Lipowska, J., Leung, E.S., Shabalin, I.G., Grabowski, M., Almo, S.C., Satchell, K.J., Joachimiak, A., Lewinski, K., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.230 (Depositor), 0.228 (DCC)
R-Value Work:
0.167 (Depositor), 0.173 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of of aldo-keto reductase from Klebsiella pneumoniae in complex with NADPH.

Lipowska, J., Leung, E.S., Shabalin, I.G., Grabowski, M., Almo, S.C., Satchell, K.J., Joachimiak, A., Lewinski, K., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 32.51 kDa
Atom Count: 2,439
Modeled Residue Count: 284
Deposited Residue Count: 285
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo/keto reductase	A	285	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: yhdN_4, yhdN, B1727_06910, B4U21_09420, BN49_2327, CAK82_20800, CQB04_18905, CR230_19100, CTI52_15935, CTI54_15930... yhdN_4, yhdN, B1727_06910, B4U21_09420, BN49_2327, CAK82_20800, CQB04_18905, CR230_19100, CTI52_15935, CTI54_15930, PMK1_03573, SAMEA3531778_00013 EC: 1.1.1
UniProt
Find proteins for A6T7Q7 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T7Q7 Go to UniProtKB: A6T7Q7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6T7Q7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.230 (Depositor), 0.228 (DCC)
R-Value Work: 0.167 (Depositor), 0.173 (DCC)
R-Value Observed: 0.171 (Depositor)

Diffraction Data:

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.626	α = 90
b = 83.626	β = 90
c = 72.834	γ = 120

Software Package:

Software Name	Purpose
MD2	data collection
HKL-3000	data scaling
SCALEPACK	data scaling
HKL-3000	data reduction
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2019-02-20
Changes: Author supporting evidence, Data collection
Version 1.2: 2022-03-23
Changes: Author supporting evidence, Database references
Version 1.3: 2023-10-04
Changes: Data collection, Refinement description