SAXSdb — 5lbg

▼

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

L,D-transpeptidase 2

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(3S)-3-HYDROXYBUTANOIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDT2_MYCTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–262； UniProt 149–408 Author chain B； PDBConstruct 3–262； UniProt 149–408

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5lbg
Deposition date deposition_date	2016-06-16
Structure title title	Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with faropenem-derived adduct at the active site cysteine-354
Keywords keywords	cell wall, peptidoglycan, transpeptidase, Mycobacterium tuberculosis, transferase; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5lbg__assembly_1__model_1

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

Download this curve (.dat)

5lbg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5lbg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.29 Å
Rg (electron density)	19.29 Å
Total Rg	20.15 Å
Atom count	1990
Residues	259
Excluded volume	34875 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5lbg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5lbg__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	L,D-transpeptidase 2
Molecular weight formula_weight	28508.6 kDa
EC 编号 ec_number	2.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4699

SMAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	83331
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	(3S)-3-HYDROXYBUTANOIC ACID
Molecular weight formula_weight	104.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	492

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5lbga1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.0 — automated matches

Domain ID domain_id	d5lbga2
Class class	b — All beta proteins
Fold Fold fold	b.160 — L,D-transpeptidase catalytic domain-like
Superfamily Superfamily superfamily	b.160.1 — L,D-transpeptidase catalytic domain-like
Family Family family	b.160.1.1 — L,D-transpeptidase catalytic domain-like

Domain ID domain_id	d5lbgb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.0 — automated matches

Domain ID domain_id	d5lbgb2
Class class	b — All beta proteins
Fold Fold fold	b.160 — L,D-transpeptidase catalytic domain-like
Superfamily Superfamily superfamily	b.160.1 — L,D-transpeptidase catalytic domain-like
Family Family family	b.160.1.1 — L,D-transpeptidase catalytic domain-like

CATH v4.4 (4 domains)

Domain ID domain_id	5lbgA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3710 —

Domain ID domain_id	5lbgA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	440 — L,D-transpeptidase catalytic domain-like
Homologous superfamily homologous superfamily	10 — L,D-transpeptidase catalytic domain-like

Domain ID domain_id	5lbgB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3710 —

Domain ID domain_id	5lbgB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	440 — L,D-transpeptidase catalytic domain-like
Homologous superfamily homologous superfamily	10 — L,D-transpeptidase catalytic domain-like

▶

Unit-cell length a length_a	45.062 Å
Unit-cell length b length_b	91.362 Å
Unit-cell length c length_c	67.550 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.540 Å
Low-resolution limit resolution_low	65.660 Å
R factor r_factor	0.1772
R_work r_work	0.1757
R_free r_free	0.2062

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with faropenem-derived adduct at the active site cysteine-354

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

L,D-transpeptidase 2

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

5lbg__assembly_1__model_1

5lbg__assembly_1__model_1 | I(q)

5lbg__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with faropenem-derived adduct at the active site cysteine-354

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

L,D-transpeptidase 2

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

5lbg__assembly_1__model_1

5lbg__assembly_1__model_1 | I(q)

5lbg__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)