SAXSdb — 3fmr

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

Methionine aminopeptidase 2

Encephalitozoon cuniculi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE (III) ION × 2 ;(1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate ; × 1 SULFATE ION × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FE (III) ION × 2 ;(1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate ; × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMPM2_ENCCU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–358； UniProt 1–358 Author chain B； PDBConstruct 1–358； UniProt 1–358

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	3fmr
Deposition date deposition_date	2008-12-22
Structure title title	Crystal structure of an Encephalitozoon cuniculi methionine aminopeptidase type 2 with angiogenesis inhibitor TNP470 bound
Keywords keywords	;METHIONINE AMINOPEPTIDASE TYPE2, METAP2, METAP2 TNP470 COMPLEX, ENCEPHALITOZOON CUNICULI, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, New York SGX Research Center for Structural Genomics, NYSGXRC, Aminopeptidase, Cobalt, Hydrolase, Metal-binding, Protease ;; 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.

3fmr__assembly_2__model_1

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

Download this curve (.dat)

3fmr__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fmr__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.88 Å
Rg (electron density)	19.88 Å
Total Rg	20.87 Å
Atom count	2798
Residues	356
Excluded volume	49659 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fmr__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fmr__assembly_2__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	Methionine aminopeptidase 2
Molecular weight formula_weight	40029.4 kDa
EC 编号 ec_number	3.4.11.18
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	5605

MKCILLNQAEELPIEFLPKDGVYGKGKLFDSRNMEIENFTESDILQDARRAAEAHRRARYRVQSIVRPGITLLEIVRSIEDSTRTLLKGERNNGIGFPAGMSMNSCAAHYTVNPGEQDIVLKEDDVLKIDFGTHSDGRIMDSAFTVAFKENLEPLLVAAREGTETGIKSLGVDVRVCDIGRDINEVISSYEVEIGGRMWPIRPISDLHGHSISQFRIHGGISIPAVNNRDTTRIKGDSFYAVETFATTGKGSIDDRPPCSHFVLNTYKSRKLFNKDLIKVYEFVKDSLGTLPFSPRHLDYYGLVKGGSLKSVNLLTMMGLLTPYPPLNDIDGCKVAQFEHTVYLSEHGKEVLTRGDDY

Source Source

Source organism organism	Encephalitozoon cuniculi
NCBI taxonomy ID ncbi_taxonomy_id	6035
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	;(1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate ;
Molecular weight formula_weight	403.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3fmrA01
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

Domain ID domain_id	3fmrA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3fmrB01
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

Domain ID domain_id	3fmrB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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Unit-cell length a length_a	61.977 Å
Unit-cell length b length_b	94.067 Å
Unit-cell length c length_c	66.407 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.33 °
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	2.890 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1830
R_work r_work	0.1780
R_free r_free	0.2660

Crystal structure of an Encephalitozoon cuniculi methionine aminopeptidase type 2 with angiogenesis inhibitor TNP470 bound

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

Methionine aminopeptidase 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

3fmr__assembly_2__model_1

3fmr__assembly_2__model_1 | I(q)

3fmr__assembly_2__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

Source Source

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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of an Encephalitozoon cuniculi methionine aminopeptidase type 2 with angiogenesis inhibitor TNP470 bound

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

Methionine aminopeptidase 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

3fmr__assembly_2__model_1

3fmr__assembly_2__model_1 | I(q)

3fmr__assembly_2__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

Source Source

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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)