SAXSdb — 3mie

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

Peptidyl-glycine alpha-amidating monooxygenase

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 2 NICKEL (II) ION × 1 SODIUM ION × 1 AZIDE ION × 3 GLYCEROL × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMD_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–314； UniProt 43–356

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	3mie
Deposition date deposition_date	2010-04-10
Structure title title	Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound azide obtained by soaking (50mM NaN3)
Keywords keywords	OXIDOREDUCTASE, MONOOXYGENASE, BIOACTIVE PEPTIDE ACTIVATION, ASCORBATE; OXIDOREDUCTASE
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.

3mie__assembly_1__model_1

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

Download this curve (.dat)

3mie__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3mie__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.90 Å
Rg (electron density)	19.85 Å
Total Rg	20.67 Å
Atom count	2449
Residues	310
Excluded volume	43540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3mie__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Peptidyl-glycine alpha-amidating monooxygenase
Molecular weight formula_weight	35008.1 kDa
EC 编号 ec_number	1.14.17.3
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	2461

FSNECLGTIGPVTPLDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEAFVIDFKPRASMDTVHHMLLFGCNMPSSTGSYWFCDEGTCTDKANILYAWARNAPPTRLPKGVGFRVGGETGSKYFVLQVHYGDISAFRDNHKDCSGVSVHLTRVPQPLIAGMYLMMSVDTVIPPGEKVVNADISCQYKMYPMHVFAYRVHTHHLGKVVSGYRVRNGQWTLIGRQNPQLPQAFYPVEHPVDVTFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKYALSFMTCTKNVAPDMFRTIPAEANIPIPV

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Cricetulus griseus

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3mieA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	310 — Copper type II, ascorbate-dependent monooxygenase, N-terminal domain

Domain ID domain_id	3mieA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	230 —

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Unit-cell length a length_a	68.719 Å
Unit-cell length b length_b	68.991 Å
Unit-cell length c length_c	81.259 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.260 Å
Low-resolution limit resolution_low	52.560 Å
R factor r_factor	0.1935
R_work r_work	0.1912
R_free r_free	0.2395

Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound azide obtained by soaking (50mM NaN3)

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

Peptidyl-glycine alpha-amidating monooxygenase

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

3mie__assembly_1__model_1

3mie__assembly_1__model_1 | I(q)

3mie__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound azide obtained by soaking (50mM NaN3)

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

Peptidyl-glycine alpha-amidating monooxygenase

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

3mie__assembly_1__model_1

3mie__assembly_1__model_1 | I(q)

3mie__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)