SAXSdb — 3d27

▼

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

Methionine aminopeptidase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 4-(3-ethylthiophen-2-yl)benzene-1,2-diol × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMPM_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–261； UniProt 4–264

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	3d27
Deposition date deposition_date	2008-05-07
Structure title title	E. coli methionine aminopeptidase with Fe inhibitor W29
Keywords keywords	;dinuclear, manganese, iron, hydrolase, peptidase, enzyme-inhibitor complex, metalloenzyme, Aminopeptidase, Cobalt, Metal-binding, Protease ;; HYDROLASE
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.

3d27__assembly_1__model_1

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

Download this curve (.dat)

3d27__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d27__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.32 Å
Rg (electron density)	17.33 Å
Total Rg	18.27 Å
Atom count	2027
Residues	261
Excluded volume	36257 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d27__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Methionine aminopeptidase
Molecular weight formula_weight	29055.4 kDa
EC 编号 ec_number	3.4.11.18
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2187

SIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVNEQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVIKDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGAAIQKFVEAEGFSVVREYCGHGIGRGFHEEPQVLHYDSRETNVVLKPGMTFTIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLRKDDTIPAIISHDE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	4-(3-ethylthiophen-2-yl)benzene-1,2-diol
Molecular weight formula_weight	220.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3d27a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

CATH v4.4 (1 domains)

Domain ID domain_id	3d27A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

▶

Unit-cell length a length_a	38.510 Å
Unit-cell length b length_b	59.880 Å
Unit-cell length c length_c	54.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	26.860 Å
R factor r_factor	0.1930
R_work r_work	0.1910
R_free r_free	0.2440

E. coli methionine aminopeptidase with Fe inhibitor W29

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

Methionine aminopeptidase

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

3d27__assembly_1__model_1

3d27__assembly_1__model_1 | I(q)

3d27__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

E. coli methionine aminopeptidase with Fe inhibitor W29

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

Methionine aminopeptidase

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

3d27__assembly_1__model_1

3d27__assembly_1__model_1 | I(q)

3d27__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)