7TZP | pdb_00007tzp

Crystal Structure of Putataive Short-Chain Dehydrogenase/Reductase (FabG) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 in Complex with NADH

PDB DOI: https://doi.org/10.2210/pdb7TZP/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-16 Released: 2022-03-02
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Satchell, K.J.F., 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: 2.60 Å
R-Value Free:
0.227 (Depositor), 0.233 (DCC)
R-Value Work:
0.189 (Depositor), 0.199 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.

Inniss, N.L., Kochan, T.J., Minasov, G., Wawrzak, Z., Chang, C., Tan, K., Shuvalova, L., Kiryukhina, O., Pshenychnyi, S., Wu, R., Dubrovska, I., Babnigg, G., Endres, M., Anderson, W.F., Hauser, A.R., Joachimiak, A., Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0101322-e0101322

PubMed: 36695589 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/mra.01013-22
Primary Citation Related Structures:
6DT3, 6DUX, 6DVV, 6DXN, 6E85, 6NAU, 6NBG, 6NDI, 6WN5, 6WN8, 6X1L, 7RJJ, 7TL5, 7TZP

PubMed Abstract:
Klebsiella pneumoniae is a leading cause of antibiotic-resistant-associated deaths in the world. Here, we report the deposition of 14 structures of enzymes from both the core and accessory genomes of sequence type 23 (ST23) K1 hypervirulent K. pneumoniae.

Organizational Affiliation

Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 215.61 kDa
Atom Count: 15,486
Modeled Residue Count: 1,962
Deposited Residue Count: 1,976
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-ACP reductase	A, B, C, D, E A, B, C, D, E, F, G, H	247	Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044	Mutation(s): 0 Gene Names: fabG_6, DBX64_14690, SAMEA4364603_02057 EC: 1.1.1.100
UniProt
Find proteins for A0A332H2K8 (Klebsiella pneumoniae) Explore A0A332H2K8 Go to UniProtKB: A0A332H2K8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A332H2K8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI (Subject of Investigation/LOI) Query on NAI Download:Ideal Coordinates CCD File SDF format, chain WA [auth G] SDF format, chain O [auth A] SDF format, chain MA [auth E] SDF format, chain AA [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain AA [auth C] mmCIF format, chain WA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain AA [auth C]	AA [auth C], MA [auth E], O [auth A], WA [auth G]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain AA [auth C] Focus chain MA [auth E] Focus chain O [auth A] Focus chain WA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain MA [auth E] Focus chain O [auth A] Focus chain WA [auth G]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth G] SDF format, chain YA [auth G] SDF format, chain XA [auth G] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain SA [auth F] SDF format, chain RA [auth F] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain NA [auth E] SDF format, chain FA [auth D] SDF format, chain EB [auth H] SDF format, chain BA [auth C] SDF format, chain AB [auth G] MOL2 format, chain ZA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth G] mmCIF format, chain ZA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth G]	AB [auth G] BA [auth C] EB [auth H] FA [auth D] NA [auth E] AB [auth G], BA [auth C], EB [auth H], FA [auth D], NA [auth E], P [auth A], Q [auth A], R [auth A], RA [auth F], SA [auth F], V [auth B], W [auth B], XA [auth G], YA [auth G], ZA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BA [auth C] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain NA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain V [auth B] Focus chain W [auth B] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain BA [auth C] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain NA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain V [auth B] Focus chain W [auth B] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain QA [auth E] SDF format, chain PA [auth E] SDF format, chain OA [auth E] SDF format, chain HB [auth H] SDF format, chain HA [auth D] SDF format, chain GB [auth H] SDF format, chain GA [auth D] SDF format, chain FB [auth H] SDF format, chain CB [auth G] SDF format, chain CA [auth C] SDF format, chain BB [auth G] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain HB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain FB [auth H] MOL2 format, chain CB [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain BB [auth G] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain OA [auth E] mmCIF format, chain HB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain FB [auth H] mmCIF format, chain CB [auth G] mmCIF format, chain CA [auth C] mmCIF format, chain BB [auth G]	BB [auth G] CA [auth C] CB [auth G] FB [auth H] GA [auth D] BB [auth G], CA [auth C], CB [auth G], FB [auth H], GA [auth D], GB [auth H], HA [auth D], HB [auth H], OA [auth E], PA [auth E], QA [auth E], S [auth A], T [auth A], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BB [auth G] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain S [auth A] Focus chain T [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain BB [auth G] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain S [auth A] Focus chain T [auth A] Focus chain X [auth B] Focus chain Y [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain TA [auth G] SDF format, chain IA [auth E] SDF format, chain I [auth A] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain IA [auth E] MOL2 format, chain I [auth A] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain IA [auth E] mmCIF format, chain I [auth A]	I [auth A], IA [auth E], TA [auth G], U [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain IA [auth E] Focus chain TA [auth G] Focus chain U [auth B] Interactions & Density Focus chain I [auth A] Focus chain IA [auth E] Focus chain TA [auth G] Focus chain U [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain VA [auth G] SDF format, chain UA [auth G] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth E] SDF format, chain L [auth A] SDF format, chain KA [auth E] SDF format, chain K [auth A] SDF format, chain JA [auth E] SDF format, chain J [auth A] SDF format, chain EA [auth D] SDF format, chain DB [auth H] SDF format, chain DA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain UA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain DA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain VA [auth G] mmCIF format, chain UA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain DA [auth D]	DA [auth D] DB [auth H] EA [auth D] J [auth A] JA [auth E] DA [auth D], DB [auth H], EA [auth D], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], N [auth A], UA [auth G], VA [auth G], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain Z [auth C]