3ekm

Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Diaminopimelate epimerase, chloroplastic

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 6 water × 6	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAPF_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–311； UniProt 52–362 Author chain B； PDBConstruct 1–311； UniProt 52–362 Author chain C； PDBConstruct 1–311； UniProt 52–362 Author chain D； PDBConstruct 1–311； UniProt 52–362 Author chain E； PDBConstruct 1–311； UniProt 52–362 Author chain F； PDBConstruct 1–311； UniProt 52–362

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ekm
Deposition date deposition_date	2008-09-19
Structure title title	Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP
Keywords keywords	;Diaminopimelate epimerase, Arabidopsis, PLP-independent amino acid racemase, aziridino-diaminopimelate, catalytic mechanism, ISOMERASE ;; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3ekm__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ekm__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ekm__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	19.12 Å
Rg (electron density)	18.24 Å
Total Rg	19.04 Å
Atom count	2183
Residues	287
Excluded volume	38660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ekm__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ekm__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ekm__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ekm__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3ekm__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3ekm__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3ekm__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Diaminopimelate epimerase, chloroplastic
Molecular weight formula_weight	34306.8 kDa
EC 编号 ec_number	5.1.1.7
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	14519

AAASMDAVTAEKFSPASFLDKKETGVLHFVKYHGLGNDFILVDNRDSSEPKITQEQAAKLCDRNFGVGADGVIFAMPGVNGTDYAMRIFNSDGSEPEMCGNGVRCFARFIAELENLQGKHSFTIHTGAGLIVPEIQDDGQVKVDMGTPILKAQDVPTKLSGNKGEAVVEAELVVDGVSWNVTCVSMGNPHCITFGKKGGPNLKVDDLNLPEIGPKFEHHEMFPARTNTEFVEVLSRSHLKMRVWERGAGATLACGTGACALVVAAVLEGRADRKCTVDLPGGPLEIEWKQEDNHIYMTGPAEAVFYGSALLHHHHHH

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1213

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3ekma1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekma2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekmb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekmb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekmc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekmc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekmd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekmd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekme1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekme2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekmf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d3ekmf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

CATH v4.4 (12 domains)

Domain ID domain_id	3ekmA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmD02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmE01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmE02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmF01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	3ekmF02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

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Unit-cell length a length_a	102.361 Å
Unit-cell length b length_b	136.606 Å
Unit-cell length c length_c	102.556 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1870
R_work r_work	0.1870
R_free r_free	0.2170

Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP

1. Protein Identity and Related Structures Protein Identity & Related Structures

Diaminopimelate epimerase, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ekm__assembly_3__model_1

3ekm__assembly_3__model_1 | I(q)

3ekm__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP

1. Protein Identity and Related Structures Protein Identity & Related Structures

Diaminopimelate epimerase, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ekm__assembly_3__model_1

3ekm__assembly_3__model_1 | I(q)

3ekm__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)