SAXSdb — 3a6d

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

Creatinine amidohydrolase

Pseudomonas putida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	MANGANESE (II) ION × 6 ZINC ION × 6 1-METHYLGUANIDINE × 6 SULFATE ION × 18 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P83772_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–260； UniProt 1–260 Author chain B； PDBConstruct 1–260； UniProt 1–260 Author chain C； PDBConstruct 1–260； UniProt 1–260 Author chain D； PDBConstruct 1–260； UniProt 1–260 Author chain E； PDBConstruct 1–260； UniProt 1–260 Author chain F； PDBConstruct 1–260； UniProt 1–260

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	3a6d
Deposition date deposition_date	2009-08-31
Structure title title	Creatininase complexed with 1-methylguanidine
Keywords keywords	creatinine amidohydrolase, urease-related amidohydrolase superfamily, closed form, 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.

3a6d__assembly_1__model_1

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

Download this curve (.dat)

3a6d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a6d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.12 Å
Rg (electron density)	33.17 Å
Total Rg	33.83 Å
Atom count	12023
Residues	1540
Excluded volume	214190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a6d__assembly_1__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	Creatinine amidohydrolase
Molecular weight formula_weight	28598.8 kDa
EC 编号 ec_number	3.5.2.10
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	13111

MSKSVFVGELTWKEYEARVAAGDCVLMLPVGALEQHGHHMCMNVDVLLPTAVCKRVAERIGALVMPGLQYGYKSQQKSGGGNHFPGTTSLDGATLTGTVQDIIRELARHGARRLVLMNGHYENSMFIVEGIDLALRELRYAGIQDFKVVVLSYWDFVKDPAVIQQLYPEGFLGWDIEHGGVFETSLMLALYPDLVDLDRVVDHPPATFPPYDVFPVDPARTPAPGTLSSAKTASREKGELILEVCVQGIADAIREEFPPT

Source Source

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	303
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	6

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	1-METHYLGUANIDINE
Molecular weight formula_weight	73.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1088

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3a6da_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.125 — Creatininase
Superfamily Superfamily superfamily	c.125.1 — Creatininase
Family Family family	c.125.1.1 — Creatininase

Domain ID domain_id	d3a6db_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.125 — Creatininase
Superfamily Superfamily superfamily	c.125.1 — Creatininase
Family Family family	c.125.1.1 — Creatininase

Domain ID domain_id	d3a6dc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.125 — Creatininase
Superfamily Superfamily superfamily	c.125.1 — Creatininase
Family Family family	c.125.1.1 — Creatininase

Domain ID domain_id	d3a6dd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.125 — Creatininase
Superfamily Superfamily superfamily	c.125.1 — Creatininase
Family Family family	c.125.1.1 — Creatininase

Domain ID domain_id	d3a6de_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.125 — Creatininase
Superfamily Superfamily superfamily	c.125.1 — Creatininase
Family Family family	c.125.1.1 — Creatininase

Domain ID domain_id	d3a6df_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.125 — Creatininase
Superfamily Superfamily superfamily	c.125.1 — Creatininase
Family Family family	c.125.1.1 — Creatininase

CATH v4.4 (6 domains)

Domain ID domain_id	3a6dA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10310 — Creatininase

Domain ID domain_id	3a6dB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10310 — Creatininase

Domain ID domain_id	3a6dC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10310 — Creatininase

Domain ID domain_id	3a6dD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10310 — Creatininase

Domain ID domain_id	3a6dE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10310 — Creatininase

Domain ID domain_id	3a6dF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10310 — Creatininase

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Unit-cell length a length_a	102.400 Å
Unit-cell length b length_b	152.700 Å
Unit-cell length c length_c	167.500 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	24

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1920
R_free r_free	0.2070

Creatininase complexed with 1-methylguanidine

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

Creatinine amidohydrolase

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

3a6d__assembly_1__model_1

3a6d__assembly_1__model_1 | I(q)

3a6d__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Creatininase complexed with 1-methylguanidine

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

Creatinine amidohydrolase

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

3a6d__assembly_1__model_1

3a6d__assembly_1__model_1 | I(q)

3a6d__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)