SAXSdb — 2zm2

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

6-aminohexanoate-dimer hydrolase

FLAVOBACTERIUM SP.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	SULFATE ION × 10 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 8 GLYCEROL × 8 water × 2	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	SULFATE ION × 5 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 GLYCEROL × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NYLC_FLASK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–21； UniProt 1–21

6-aminohexanoate-dimer hydrolase

FLAVOBACTERIUM SP.

UniProt P07062

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	SULFATE ION × 10 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 8 GLYCEROL × 8 water × 2	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	SULFATE ION × 5 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 GLYCEROL × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NYLC_FLASK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–392； UniProt 22–392

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	2zm2
Deposition date deposition_date	2008-04-10
Structure title title	Structure of 6-aminohexanoate-dimer hydrolase, A61V/A124V/R187S/F264C/G291R/G338A/D370Y mutant (Hyb-S4M94)
Keywords keywords	ALPHA-BETA, 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.

2zm2__assembly_1__model_1

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

Download this curve (.dat)

2zm2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zm2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.46 Å
Rg (electron density)	27.54 Å
Total Rg	28.28 Å
Atom count	6124
Residues	768
Excluded volume	107030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zm2__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zm2__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	6-aminohexanoate-dimer hydrolase
Molecular weight formula_weight	42943.7 kDa
EC 编号 ec_number	3.5.1.46
Mutation mutation	A61V, A124V, R187S, F264C, G291R, G338A, D370Y
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	3557

MNARSTGQHPARYPGAAAGEPTLDSWQEPPHNRWAFAHLGEMVPSAAVSRRPVNAPGHALVRLGAIAAQLPDLEQRLEQTYTDAFLVLRGTEVVAEYYRAGFAPDDRHLLMSVSKSLCGTVVGVLVDEGRIDPAQPVTEYVPELAGSVYDGPSVLQVLDMQISIDYNEDYVDPASEVQTHGRSAGWSTRRHGDPADTYEFLTTLRGDGSTGEFQYCSANTDVLAWIVERVTGLRYVEALSTYLWAKLDADRDATITVDTTGFGCAHGGVSCTARDLARVGRMMLDGGVAPRGRVVSEDWVRRVLAGGSHEAMTDKGFTNTFPDGSYTRQWWCTGNERANVSGIGIHGQNLWLDPLTDSVIVKLSSWPDPYTEHWHRLQNGILLDVSRALDAV

Source Source

Source organism organism	FLAVOBACTERIUM SP.
NCBI taxonomy ID ncbi_taxonomy_id	239
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	495

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2zm2a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (3 domains)

Domain ID domain_id	2zm2A01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 —

Domain ID domain_id	2zm2A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2zm2A03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	710 —

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Unit-cell length a length_a	96.442 Å
Unit-cell length b length_b	96.442 Å
Unit-cell length c length_c	113.496 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	33.640 Å
R factor r_factor	0.1790
R_work r_work	0.1790
R_free r_free	0.1920

Structure of 6-aminohexanoate-dimer hydrolase, A61V/A124V/R187S/F264C/G291R/G338A/D370Y mutant (Hyb-S4M94)

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

6-aminohexanoate-dimer hydrolase

State in the Current Structure

Other States of the Same Protein in the Database

6-aminohexanoate-dimer hydrolase

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

2zm2__assembly_1__model_1

2zm2__assembly_1__model_1 | I(q)

2zm2__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 (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

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structure of 6-aminohexanoate-dimer hydrolase, A61V/A124V/R187S/F264C/G291R/G338A/D370Y mutant (Hyb-S4M94)

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

6-aminohexanoate-dimer hydrolase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

6-aminohexanoate-dimer hydrolase

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

2zm2__assembly_1__model_1

2zm2__assembly_1__model_1 | I(q)

2zm2__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 (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

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)