SAXSdb — 1u10

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

Penicillin-insensitive murein endopeptidase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 3 SULFATE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 3 SULFATE ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 3 SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MEPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–255； UniProt 20–274 Author chain B； PDBConstruct 1–255； UniProt 20–274 Author chain C； PDBConstruct 1–255； UniProt 20–274 Author chain D； PDBConstruct 1–255； UniProt 20–274 Author chain E； PDBConstruct 1–255； UniProt 20–274 Author chain F； PDBConstruct 1–255； UniProt 20–274

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	1u10
Deposition date deposition_date	2004-07-14
Structure title title	MEPA, active form with ZN in P1
Keywords keywords	LAS enzyme, metallopeptidase, peptidoglycan hydrolase, hydrolase; 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.

1u10__assembly_3__model_1

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

Download this curve (.dat)

1u10__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1u10__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	30.57 Å
Rg (electron density)	30.63 Å
Total Rg	30.97 Å
Atom count	3776
Residues	469
Excluded volume	67006 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1u10__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1u10__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1u10__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	Penicillin-insensitive murein endopeptidase
Molecular weight formula_weight	28612.8 kDa
EC 编号 ec_number	3.4.99.-
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	11311

ATPWQKITQPVPGSAQSIGSFSNGCIVGADTLPIQSEHYQVMRTDQRRYFGHPDLVMFIQRLSSQVSNLGMGTVLIGDMGMPAGGRFNGGHASHQTGLDVDIFLQLPKTRWTSAQLLRPQALDLVSRDGKHVVSTLWKPEIFSLIKLAAQDKDVTRIFVNPAIKQQLCLDAGTDRDWLRKVRPWFQHRAHMHVRLRCPADSLECEDQPLPPSGDGCGAELQSWFEPPKPGTTKPEKKTPPPLPPSCQALLDEHVI

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	9

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	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	55

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1u10a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
Family Family family	d.65.1.3 — MepA-like

Domain ID domain_id	d1u10b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
Family Family family	d.65.1.3 — MepA-like

Domain ID domain_id	d1u10c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
Family Family family	d.65.1.3 — MepA-like

Domain ID domain_id	d1u10d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
Family Family family	d.65.1.3 — MepA-like

Domain ID domain_id	d1u10e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
Family Family family	d.65.1.3 — MepA-like

Domain ID domain_id	d1u10f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
Family Family family	d.65.1.3 — MepA-like

CATH v4.4 (6 domains)

Domain ID domain_id	1u10A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1u10B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1u10C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1u10D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1u10E00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1u10F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	35.613 Å
Unit-cell length b length_b	77.988 Å
Unit-cell length c length_c	127.663 Å
Unit-cell angle α angle_alpha	93.15 °
Unit-cell angle β angle_beta	95.93 °
Unit-cell angle γ angle_gamma	90.75 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2355
R_work r_work	0.2339
R_free r_free	0.2658

MEPA, active form with ZN in P1

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

Penicillin-insensitive murein endopeptidase

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

1u10__assembly_3__model_1

1u10__assembly_3__model_1 | I(q)

1u10__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

MEPA, active form with ZN in P1

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

Penicillin-insensitive murein endopeptidase

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

1u10__assembly_3__model_1

1u10__assembly_3__model_1 | I(q)

1u10__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)