8ZN4 | pdb_00008zn4

Crystal structure of Poly(ethylene glycol) stabilized erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 2.30 A resolution

PDB DOI: https://doi.org/10.2210/pdb8ZN4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-25 Released: 2024-06-05
Deposition Author(s): Viswanathan, V., Kumari, A., Singh, A., Kumar, A., Sharma, P., Chopra, S., Sharma, S., Raje, C.I., Singh, T.P.
Funding Organization(s): Science and Engineering Research Board (SERB), Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.201 (Depositor), 0.188 (DCC)
R-Value Work:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Poly(ethylene glycol) stabilized erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 2.30 A resolution

Viswanathan, V., Kumari, A., Singh, A., Kumar, A., Sharma, P., Chopra, S., Sharma, S., Raje, C.I., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 159.7 kDa
Atom Count: 11,897
Modeled Residue Count: 1,364
Deposited Residue Count: 1,364
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	341	Acinetobacter baumannii	Mutation(s): 0 Gene Names: epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760... epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_18430, EA706_09520, EA720_004470, EGM95_14355, F4T85_07645, FDN00_13975, FE003_13215, FJU42_18405, FJV09_11310, GSE42_06795, HBK86_03865, IAG11_16195, SAMEA4394745_03679 EC: 1.2.1

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain IA [auth C] SDF format, chain RA [auth D] SDF format, chain V [auth B] MOL2 format, chain E [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain V [auth B] mmCIF format, chain E [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain RA [auth D] mmCIF format, chain V [auth B]	E [auth A], IA [auth C], RA [auth D], V [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain IA [auth C] Focus chain RA [auth D] Focus chain V [auth B] Interactions & Density Focus chain E [auth A] Focus chain IA [auth C] Focus chain RA [auth D] Focus chain V [auth B]
XPE (Subject of Investigation/LOI) Query on XPE Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C₂₀ H₄₂ O₁₁ DTPCFIHYWYONMD-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
PG4 (Subject of Investigation/LOI) Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain JA [auth C] SDF format, chain MA [auth C] SDF format, chain WA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain WA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain WA [auth D]	CA [auth B] G [auth A] GA [auth B] JA [auth C] MA [auth C] CA [auth B], G [auth A], GA [auth B], JA [auth C], MA [auth C], WA [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain JA [auth C] Focus chain MA [auth C] Focus chain WA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain JA [auth C] Focus chain MA [auth C] Focus chain WA [auth D]
PGE (Subject of Investigation/LOI) Query on PGE Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain S [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain S [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain S [auth A]	HA [auth C], S [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain S [auth A] Interactions & Density Focus chain HA [auth C] Focus chain S [auth A]
TRS (Subject of Investigation/LOI) Query on TRS Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth B] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B] mmCIF format, chain K [auth A] mmCIF format, chain U [auth B]	K [auth A], U [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain K [auth A] Focus chain U [auth B] Interactions & Density Focus chain K [auth A] Focus chain U [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain F [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain QA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	DA [auth B] F [auth A] L [auth A] LA [auth C] QA [auth D] DA [auth B], F [auth A], L [auth A], LA [auth C], QA [auth D], Y [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain F [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain QA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain DA [auth B] Focus chain F [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain QA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain PA [auth C] SDF format, chain T [auth A] SDF format, chain XA [auth D] MOL2 format, chain PA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain XA [auth D] mmCIF format, chain PA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain XA [auth D]	PA [auth C], T [auth A], XA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain PA [auth C] Focus chain T [auth A] Focus chain XA [auth D] Interactions & Density Focus chain PA [auth C] Focus chain T [auth A] Focus chain XA [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain OA [auth C] SDF format, chain Q [auth A] SDF format, chain ZA [auth D] SDF format, chain EA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain ZA [auth D] MOL2 format, chain EA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain OA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain ZA [auth D] mmCIF format, chain EA [auth B]	AA [auth B], EA [auth B], OA [auth C], Q [auth A], ZA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain EA [auth B] Focus chain OA [auth C] Focus chain Q [auth A] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain EA [auth B] Focus chain OA [auth C] Focus chain Q [auth A] Focus chain ZA [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain FA [auth B] SDF format, chain H [auth A] SDF format, chain KA [auth C] SDF format, chain M [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain VA [auth D] SDF format, chain X [auth B] SDF format, chain YA [auth D] SDF format, chain UA [auth D] SDF format, chain N [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	AB [auth D] BA [auth B] FA [auth B] H [auth A] I [auth A] AB [auth D], BA [auth B], FA [auth B], H [auth A], I [auth A], J [auth A], KA [auth C], M [auth A], N [auth A], NA [auth C], O [auth A], P [auth A], SA [auth D], TA [auth D], UA [auth D], VA [auth D], X [auth B], YA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain BA [auth B] Focus chain FA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain X [auth B] Focus chain YA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BA [auth B] Focus chain FA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain X [auth B] Focus chain YA [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]