2xln

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-{[(2,6-DIMETHOXYPHENYL)CARBONYL]AMINO}ETHYL]BORONIC ACID × 1 SULFATE ION × 4 COBALT (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	[(1S)-1-{[(2,6-DIMETHOXYPHENYL)CARBONYL]AMINO}ETHYL]BORONIC ACID × 1 SULFATE ION × 5 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	[(1S)-1-{[(2,6-DIMETHOXYPHENYL)CARBONYL]AMINO}ETHYL]BORONIC ACID × 1 SULFATE ION × 4 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	[(1S)-1-{[(2,6-DIMETHOXYPHENYL)CARBONYL]AMINO}ETHYL]BORONIC ACID × 1 SULFATE ION × 4 COBALT (II) ION × 1 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 1–489； UniProt 50–538 Author chain B； PDBConstruct 1–489； UniProt 50–538 Author chain C； PDBConstruct 1–489； UniProt 50–538 Author chain D； PDBConstruct 1–489； UniProt 50–538

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	2xln
Deposition date deposition_date	2010-07-21
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.

2xln__assembly_1__model_1

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

Download this curve (.dat)

2xln__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xln__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.27 Å
Rg (electron density)	24.30 Å
Total Rg	25.02 Å
Atom count	3392
Residues	467
Excluded volume	59265 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xln__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2xln__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2xln__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2xln__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	50083.8 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	14369

RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPEGARMMRGPVQGSGELECSWVQAC

Entity 2 Entity 2 non-polymer

Description description	[(1S)-1-{[(2,6-DIMETHOXYPHENYL)CARBONYL]AMINO}ETHYL]BORONIC ACID
Molecular weight formula_weight	253.1 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	17

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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	816

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2xlna_
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	d2xlnb_
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	d2xlnc_
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	d2xlnd_
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	2xlnA01
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	2xlnA02
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	2xlnB01
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	2xlnB02
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	2xlnC01
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	2xlnC02
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	2xlnD01
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	2xlnD02
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	102.994 Å
Unit-cell length b length_b	91.258 Å
Unit-cell length c length_c	106.878 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	33.350 Å
R factor r_factor	0.1942
R_work r_work	0.1914
R_free r_free	0.2472

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

2xln__assembly_1__model_1

2xln__assembly_1__model_1 | I(q)

2xln__assembly_1__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

2xln__assembly_1__model_1

2xln__assembly_1__model_1 | I(q)

2xln__assembly_1__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)