1b65

Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold

Method: X-RAY DIFFRACTION

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

PROTEIN (AMINOPEPTIDASE)

Ochrobactrum anthropi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q59632_OCHAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–375； UniProt 1–375 Author chain B； PDBConstruct 1–375； UniProt 1–375 Author chain C； PDBConstruct 1–375； UniProt 1–375 Author chain D； PDBConstruct 1–375； UniProt 1–375 Author chain E； PDBConstruct 1–375； UniProt 1–375 Author chain F； PDBConstruct 1–375； UniProt 1–375

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	1b65
Deposition date deposition_date	1999-01-20
Structure title title	Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold
Keywords keywords	HYDROLASE, PEPTIDE DEGRADATION, NTN 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.

1b65__assembly_1__model_1

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

Download this curve (.dat)

1b65__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1b65__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.07 Å
Rg (electron density)	30.88 Å
Total Rg	31.63 Å
Atom count	10988
Residues	1452
Excluded volume	193430 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1b65__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1b65__assembly_2__model_1`	tetrameric （4）	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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1b65a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

Domain ID domain_id	d1b65f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.154 — DmpA/ArgJ-like
Superfamily Superfamily superfamily	d.154.1 — DmpA/ArgJ-like
Family Family family	d.154.1.1 — DmpA-like

CATH v4.4 (6 domains)

Domain ID domain_id	1b65A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65B00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65C00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65D00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65E00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

Domain ID domain_id	1b65F00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	70 — L-amino peptidase D-ALA esterase/amidase
Homologous superfamily homologous superfamily	12 — L-amino peptidase D-ALA esterase/amidase

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Unit-cell length a length_a	156.970 Å
Unit-cell length b length_b	96.220 Å
Unit-cell length c length_c	154.410 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.820 Å
Low-resolution limit resolution_low	12.500 Å
R factor r_factor	0.1700
R_work r_work	0.1690
R_free r_free	0.2060

Description description	PROTEIN (AMINOPEPTIDASE)
Molecular weight formula_weight	40457.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17786

Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold

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

PROTEIN (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

1b65__assembly_1__model_1

1b65__assembly_1__model_1 | I(q)

1b65__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (3)

Source organism organism	Ochrobactrum anthropi
NCBI taxonomy ID ncbi_taxonomy_id	529
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1304

Structure of l-aminopeptidase d-ala-esterase/amidase from ochrobactrum anthropi, a prototype for the serine aminopeptidases, reveals a new variant among the ntn hydrolase fold

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

PROTEIN (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

1b65__assembly_1__model_1

1b65__assembly_1__model_1 | I(q)

1b65__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (3)