10LI | pdb_000010li

D-Ornithine/D-lysine decarboxylase complexed with putrescine and agmatine

PDB DOI: https://doi.org/10.2210/pdb10LI/pdb

Classification: LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-01-26 Released: 2026-02-11
Deposition Author(s): Phillips, R.S., Blankenship, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.180 (Depositor), 0.181 (DCC)
R-Value Work:
0.141 (Depositor), 0.141 (DCC)
R-Value Observed:
0.143 (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

D-Ornithine/D-lysine decarboxylase complexed with putrescine and agmatine

Phillips, R.S., Blankenship, S.

To be published.

Macromolecule Content

Total Structure Weight: 55.33 kDa
Atom Count: 4,781
Modeled Residue Count: 462
Deposited Residue Count: 478
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A	478	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: lysA_1, A3Y76_06550, AAB27_07220, AU613_21760, AVC05_12620, B1P38_05720, CE70_14345, CFF59_15330, DD95_01965, DMO92_13220... lysA_1, A3Y76_06550, AAB27_07220, AU613_21760, AVC05_12620, B1P38_05720, CE70_14345, CFF59_15330, DD95_01965, DMO92_13220, DPF41_09855, DPS76_08380, DRM14_11030, DU071_05960, E0935_14000, EER35_06850, F3R12_16115, GB466_10640, SE14_02571
UniProt
Find proteins for A0A0D6FAR3 (Salmonella typhimurium) Explore A0A0D6FAR3 Go to UniProtKB: A0A0D6FAR3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0D6FAR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AG2 (Subject of Investigation/LOI) Query on AG2 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	AGMATINE C₅ H₁₄ N₄ QYPPJABKJHAVHS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PUT (Subject of Investigation/LOI) Query on PUT Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain I [auth A] MOL2 format, chain B [auth A] MOL2 format, chain I [auth A] mmCIF format, chain B [auth A] mmCIF format, chain I [auth A]	B [auth A], I [auth A]	1,4-DIAMINOBUTANE C₄ H₁₂ N₂ KIDHWZJUCRJVML-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain I [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain H [auth A]	C [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain H [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]