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5du7

Crystal structure of ldtMt2 at 1.79 Angstrom resolution

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

L,D-transpeptidase 2

Mycobacterium tuberculosis

UniProt O53223

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 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count
5 Protein homooligomer Homooligomer Protein 2 water × 2 Consistent with protein count
6 Protein homooligomer Homooligomer Protein 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3tur 3tur 3tx4 3tx4 3u1p 3u1p 3u1q 3u1q 3vae 3vae 3vyn 3vyn

57 assemblies; showing the first 12

Homodimer
3tur 3tx4 3u1p 3u1q 3vae 3vyo 4gsu 5du7 5du7 5duj 8bk3

11 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
8pxy 8pxz

2 assemblies

View Construct and Data Evidence
UniProt name LDT2_MYCTO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–370； UniProt 42–408 Author chain B； PDBConstruct 4–370； UniProt 42–408 Author chain C； PDBConstruct 4–370； UniProt 42–408 Author chain D； PDBConstruct 4–370； UniProt 42–408

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id5du7
Deposition date deposition_date2015-09-18
Structure title titleCrystal structure of ldtMt2 at 1.79 Angstrom resolution
Keywords keywordsPeptidoglycan synthesis enzyme, cell wall enzyme, TRANSFERASE; TRANSFERASE
Experimental Method methodX-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.

5du7__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5du7__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5du7__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）27.01 Å
Rg (electron density)27.00 Å
Total Rg27.61 Å
Atom count2633
Residues349
Excluded volume46231 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5du7__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5du7__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5du7__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5du7__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 5du7__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 5du7__assembly_6__model_1 dimeric （2） 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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id5du7A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily3710 —
Domain ID domain_id5du7A03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology440 — L,D-transpeptidase catalytic domain-like
Homologous superfamily homologous superfamily10 — L,D-transpeptidase catalytic domain-like
Domain ID domain_id5du7B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily3710 —
Domain ID domain_id5du7B03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology440 — L,D-transpeptidase catalytic domain-like
Homologous superfamily homologous superfamily10 — L,D-transpeptidase catalytic domain-like
Domain ID domain_id5du7C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily3710 —
Domain ID domain_id5du7C03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology440 — L,D-transpeptidase catalytic domain-like
Homologous superfamily homologous superfamily10 — L,D-transpeptidase catalytic domain-like
Domain ID domain_id5du7D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily3710 —
Domain ID domain_id5du7D03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology440 — L,D-transpeptidase catalytic domain-like
Homologous superfamily homologous superfamily10 — L,D-transpeptidase catalytic domain-like
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7. Citations (1)