7T1Q

Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic Acid

PDB DOI: https://doi.org/10.2210/pdb7T1Q/pdb

Classification: HYDROLASE
Organism(s): Acinetobacter baumannii ATCC 17978
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-12-02 Released: 2021-12-15
Deposition Author(s): Minasov, G., Shuvalova, L., Brunzelle, J.S., Dubrovska, I., Pshenychnyi, S., 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: 2.25 Å
R-Value Free: 0.233
R-Value Work: 0.188
R-Value Observed: 0.190

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 the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic Acid.

Minasov, G., Shuvalova, L., Brunzelle, J.S., Dubrovska, I., Pshenychnyi, S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 83.7 kDa
Atom Count: 6,194
Modelled Residue Count: 752
Deposited Residue Count: 756
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-diaminopimelate desuccinylase	A, B	378	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Gene Names: dapE, A1S_2810 EC: 3.5.1.18
UniProt
Find proteins for A3M8H2 (Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M8H2 Go to UniProtKB: A3M8H2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M8H2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SIN (Subject of Investigation/LOI) Query on SIN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	F [auth A], G [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B]	D [auth A], I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]