9IIM

Structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with nicotinamide adenine dinucleotide at 2.74 A resolution.

PDB DOI: https://doi.org/10.2210/pdb9IIM/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: 2.74 Å
R-Value Free: 0.229
R-Value Work: 0.164

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 at 2.74 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: 155.29 kDa
Atom Count: 11,379
Modelled Residue Count: 1,364
Deposited Residue Count: 1,364
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B [auth C], C [auth B], 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 A0A059ZTK9 (Acinetobacter baumannii) Explore A0A059ZTK9 Go to UniProtKB: A0A059ZTK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A059ZTK9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 I [auth B] SDF format, chain G [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain G [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain G [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth C], I [auth B], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth B] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth B] Focus chain K [auth D]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth C] SDF format, chain J [auth B] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain J [auth B] mmCIF format, chain L [auth D]	F [auth A], H [auth C], J [auth B], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth B] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth B] Focus chain L [auth D]