9IIL | pdb_00009iil

Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide in the presence of poly(ethylene glycol) at 2.20 A resolution

PDB DOI: https://doi.org/10.2210/pdb9IIL/pdb

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

Deposited: 2024-06-20 Released: 2024-07-03
Deposition Author(s): Viswanathan, V., Kumari, A., Singh, A., Kumar, A., Sharma, P., Chopra, S., Jeyakanthan, J., 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: 2.20 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.168 (Depositor), 0.175 (DCC)

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

Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide in the presence of poly(ethylene glycol) at 2.20 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 158.96 kDa
Atom Count: 11,823
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
UniProt
Find proteins for A0A0D5YKI8 (Acinetobacter baumannii) Explore A0A0D5YKI8 Go to UniProtKB: A0A0D5YKI8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0D5YKI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 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 P [auth B] SDF format, chain KA [auth D] SDF format, chain E [auth A] SDF format, chain CA [auth C] MOL2 format, chain P [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth C] mmCIF format, chain P [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth C]	CA [auth C], E [auth A], KA [auth D], P [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain CA [auth C] Focus chain E [auth A] Focus chain KA [auth D] Focus chain P [auth B] Interactions & Density Focus chain CA [auth C] Focus chain E [auth A] Focus chain KA [auth D] Focus chain P [auth B]
1PE (Subject of Investigation/LOI) Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain LA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain LA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain LA [auth D]	LA [auth D], Q [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain LA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain LA [auth D] Focus chain Q [auth B]
PG4 (Subject of Investigation/LOI) Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain G [auth A] SDF format, chain DA [auth C] SDF format, chain AA [auth B] MOL2 format, chain R [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain R [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain AA [auth B]	AA [auth B] DA [auth C] G [auth A] N [auth A] O [auth A] AA [auth B], DA [auth C], G [auth A], N [auth A], O [auth A], R [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain DA [auth C] Focus chain G [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Interactions & Density Focus chain AA [auth B] Focus chain DA [auth C] Focus chain G [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B]
PGE (Subject of Investigation/LOI) Query on PGE Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain L [auth A] SDF format, chain EA [auth C] SDF format, chain BA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain BA [auth C]	BA [auth C], EA [auth C], L [auth A], W [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain EA [auth C] Focus chain L [auth A] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain EA [auth C] Focus chain L [auth A] Focus chain W [auth B]
TRS (Subject of Investigation/LOI) Query on TRS Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain IA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth C]	IA [auth C], M [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain IA [auth C] Focus chain M [auth A] Interactions & Density Focus chain IA [auth C] Focus chain M [auth A]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain JA [auth D] SDF format, chain GA [auth C] SDF format, chain F [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain F [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain F [auth A]	F [auth A] GA [auth C] JA [auth D] T [auth B] U [auth B] F [auth A], GA [auth C], JA [auth D], T [auth B], U [auth B], Y [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain GA [auth C] Focus chain JA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth B] Interactions & Density Focus chain F [auth A] Focus chain GA [auth C] Focus chain JA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth B]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain V [auth B] SDF format, chain S [auth B] SDF format, chain PA [auth D] SDF format, chain OA [auth D] SDF format, chain NA [auth D] SDF format, chain MA [auth D] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain FA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain V [auth B] MOL2 format, chain S [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain FA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain V [auth B] mmCIF format, chain S [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain FA [auth C]	FA [auth C] H [auth A] HA [auth C] I [auth A] J [auth A] FA [auth C], H [auth A], HA [auth C], I [auth A], J [auth A], MA [auth D], NA [auth D], OA [auth D], PA [auth D], S [auth B], V [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain S [auth B] Focus chain V [auth B] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain S [auth B] Focus chain V [auth B] Focus chain Z [auth B]