3pva

PENICILLIN V ACYLASE FROM B. SPHAERICUS

Method: X-RAY DIFFRACTION

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

PROTEIN (PENICILLIN V ACYLASE)

OrganismNot specified

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	PAC_BACSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–335； UniProt 4–338 Author chain B； PDBConstruct 1–335； UniProt 4–338 Author chain C； PDBConstruct 1–335； UniProt 4–338 Author chain D； PDBConstruct 1–335； UniProt 4–338 Author chain E； PDBConstruct 1–335； UniProt 4–338 Author chain F； PDBConstruct 1–335； UniProt 4–338 Author chain G； PDBConstruct 1–335； UniProt 4–338 Author chain H； PDBConstruct 1–335； UniProt 4–338

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	3pva
Deposition date deposition_date	1998-11-13
Structure title title	PENICILLIN V ACYLASE FROM B. SPHAERICUS
Keywords keywords	AMIDOHYDROLASE, NTN HYDROLASE, PENICILLIN V ACYLASE, 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.

3pva__assembly_1__model_1

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

Download this curve (.dat)

3pva__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pva__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.07 Å
Rg (electron density)	34.27 Å
Total Rg	34.90 Å
Atom count	10420
Residues	1336
Excluded volume	186260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pva__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pva__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) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3pvaa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.3 — Penicillin V acylase

Domain ID domain_id	d3pvab_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.3 — Penicillin V acylase

Domain ID domain_id	d3pvac_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.3 — Penicillin V acylase

Domain ID domain_id	d3pvad_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.3 — Penicillin V acylase

Domain ID domain_id	d3pvae_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.3 — Penicillin V acylase

Domain ID domain_id	d3pvaf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.3 — Penicillin V acylase

Domain ID domain_id	d3pvag_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.3 — Penicillin V acylase

Domain ID domain_id	d3pvah_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.3 — Penicillin V acylase

CATH v4.4 (8 domains)

Domain ID domain_id	3pvaA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	60 — Penicillin V Acylase; Chain A
Homologous superfamily homologous superfamily	10 — Penicillin V Acylase; Chain A

Domain ID domain_id	3pvaB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	60 — Penicillin V Acylase; Chain A
Homologous superfamily homologous superfamily	10 — Penicillin V Acylase; Chain A

Domain ID domain_id	3pvaC00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	60 — Penicillin V Acylase; Chain A
Homologous superfamily homologous superfamily	10 — Penicillin V Acylase; Chain A

Domain ID domain_id	3pvaD00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	60 — Penicillin V Acylase; Chain A
Homologous superfamily homologous superfamily	10 — Penicillin V Acylase; Chain A

Domain ID domain_id	3pvaE00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	60 — Penicillin V Acylase; Chain A
Homologous superfamily homologous superfamily	10 — Penicillin V Acylase; Chain A

Domain ID domain_id	3pvaF00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	60 — Penicillin V Acylase; Chain A
Homologous superfamily homologous superfamily	10 — Penicillin V Acylase; Chain A

Domain ID domain_id	3pvaG00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	60 — Penicillin V Acylase; Chain A
Homologous superfamily homologous superfamily	10 — Penicillin V Acylase; Chain A

Domain ID domain_id	3pvaH00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	60 — Penicillin V Acylase; Chain A
Homologous superfamily homologous superfamily	10 — Penicillin V Acylase; Chain A

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Unit-cell length a length_a	47.400 Å
Unit-cell length b length_b	129.600 Å
Unit-cell length c length_c	156.700 Å
Unit-cell angle α angle_alpha	88.30 °
Unit-cell angle β angle_beta	83.40 °
Unit-cell angle γ angle_gamma	84.60 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	14.000 Å
R factor r_factor	—
R_work r_work	0.2110
R_free r_free	0.2430

Description description	PROTEIN (PENICILLIN V ACYLASE)
Molecular weight formula_weight	37189.1 kDa
EC 编号 ec_number	3.5.1.11
Source method src_method	nat
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	23640

PENICILLIN V ACYLASE FROM B. SPHAERICUS

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

PROTEIN (PENICILLIN V ACYLASE)

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

3pva__assembly_1__model_1

3pva__assembly_1__model_1 | I(q)

3pva__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

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2800

PENICILLIN V ACYLASE FROM B. SPHAERICUS

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

PROTEIN (PENICILLIN V ACYLASE)

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

3pva__assembly_1__model_1

3pva__assembly_1__model_1 | I(q)

3pva__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

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)