2xk1

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

Method: X-RAY DIFFRACTION

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

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	[(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-) × 1 SULFATE ION × 4 COBALT (II) ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	[(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-) × 1 SULFATE ION × 4 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	[(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-) × 1 SULFATE ION × 4 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	[(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-) × 1 SULFATE ION × 4 COBALT (II) ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAC_ACTSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–466； UniProt 50–515 Author chain B； PDBConstruct 1–466； UniProt 50–515 Author chain C； PDBConstruct 1–466； UniProt 50–515 Author chain D； PDBConstruct 1–466； UniProt 50–515

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	2xk1
Deposition date deposition_date	2010-07-07
Structure title title	Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor
Keywords keywords	HYDROLASE, PEPTIDOGLYCAN; HYDROLASE
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.

2xk1__assembly_3__model_1

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

Download this curve (.dat)

2xk1__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xk1__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.25 Å
Rg (electron density)	24.28 Å
Total Rg	25.04 Å
Atom count	3384
Residues	465
Excluded volume	59155 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xk1__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2xk1__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2xk1__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2xk1__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
Molecular weight formula_weight	47647.0 kDa
EC 编号 ec_number	3.4.16.4
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13724

RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE

Entity 2 Entity 2 non-polymer

Description description	[(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-)
Molecular weight formula_weight	300.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	166

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2xk1a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.3 — Dac-like

Domain ID domain_id	d2xk1b_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.3 — Dac-like

Domain ID domain_id	d2xk1c_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.3 — Dac-like

Domain ID domain_id	d2xk1d_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.3 — Dac-like

CATH v4.4 (8 domains)

Domain ID domain_id	2xk1A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2xk1A02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

Domain ID domain_id	2xk1B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2xk1B02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

Domain ID domain_id	2xk1C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2xk1C02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

Domain ID domain_id	2xk1D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2xk1D02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

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Unit-cell length a length_a	154.898 Å
Unit-cell length b length_b	92.348 Å
Unit-cell length c length_c	143.829 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	27.530 Å
R factor r_factor	0.2190
R_work r_work	0.2170
R_free r_free	0.2640

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

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

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

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

2xk1__assembly_3__model_1

2xk1__assembly_3__model_1 | I(q)

2xk1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

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

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

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

2xk1__assembly_3__model_1

2xk1__assembly_3__model_1 | I(q)

2xk1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)