SAXSdb — 5ib9

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

Aminopeptidase

Aneurinibacillus sp. AM-1

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 × 12 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A2V759_9BACL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–421； UniProt 36–456

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	5ib9
Deposition date deposition_date	2016-02-22
Structure title title	Crystal structure of aminopeptidase equipped with PAD from Aneurinibacillus sp. AM-1
Keywords keywords	Aminopeptidase Protease-associated domain Homo-dimerization Inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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.

5ib9__assembly_1__model_1

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

Download this curve (.dat)

5ib9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ib9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.77 Å
Rg (electron density)	29.91 Å
Total Rg	30.75 Å
Atom count	6294
Residues	824
Excluded volume	111800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ib9__assembly_1__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	Aminopeptidase
Molecular weight formula_weight	45289.7 kDa
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	3737

APAHADHQITKRTDAENMYNTIQFLSQAPRVAGSPEELKAVRYIEQQFKSYGYHVEVQPFQFEGYTAPSEVTLKIGTEKKEGEAFTYSPNSDVTAELVYVGLGTTADVAGKDLNGKIALIQRGNISFADKVRNAAKQGAKAVIIYNNTDGKLNGTLGGSDASFVAAVGITKQEGDALAANLRAGEKITATVKVAGAEVKTLTSHNVIATKKPDANKKNTNDIIIIGSHHDSVEKAPGANDDASGVAVTLELARVMSKLKTDTELRFITFGAEENGLIGSKKYAASLSEDEIKRTIGMFQLDMVGSKDAGDLIMYTIDGKKNRVTDLGAAASSRLSGVLPYGQEGRSDHESFHALGIPAALFIHAPVEPWYHTPNDTLDKISKEKLDNVADIVGSAVYQAARPGELVIEPIDYPRRNVELQN

Source Source

Source organism organism	Aneurinibacillus sp. AM-1
NCBI taxonomy ID ncbi_taxonomy_id	400761
Host organism host_organism	Escherichia coli

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	6

Entity 3 Entity 3 non-polymer

Description description	2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
Molecular weight formula_weight	308.4 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	590

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ib9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	5ib9A02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	93.180 Å
Unit-cell length b length_b	68.443 Å
Unit-cell length c length_c	76.589 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	39.800 Å
R factor r_factor	0.1809
R_work r_work	0.1787
R_free r_free	0.2228

Crystal structure of aminopeptidase equipped with PAD from Aneurinibacillus sp. AM-1

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

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

5ib9__assembly_1__model_1

5ib9__assembly_1__model_1 | I(q)

5ib9__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 (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

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of aminopeptidase equipped with PAD from Aneurinibacillus sp. AM-1

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

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

5ib9__assembly_1__model_1

5ib9__assembly_1__model_1 | I(q)

5ib9__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 (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

CATH v4.4 (2 domains)

7. Citations (1)