SAXSdb — 1lfw

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

pepV

Lactobacillus delbrueckii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 3-[(1-AMINO-2-CARBOXY-ETHYL)-HYDROXY-PHOSPHINOYL]-2-METHYL-PROPIONIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEPV_LACDL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–470； UniProt 1–470

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	1lfw
Deposition date deposition_date	2002-04-12
Structure title title	Crystal structure of pepV
Keywords keywords	Hydrolase, Dipeptidase; 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.

1lfw__assembly_1__model_1

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

Download this curve (.dat)

1lfw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1lfw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.05 Å
Rg (electron density)	23.51 Å
Total Rg	24.20 Å
Atom count	3668
Residues	468
Excluded volume	65087 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1lfw__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	pepV
Molecular weight formula_weight	52045.1 kDa
EC 编号 ec_number	3.4.13.3
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	4238

MDLNFKELAEAKKDAILKDLEELIAIDSSEDLENATEEYPVGKGPVDAMTKFLSFAKRDGFDTENFANYAGRVNFGAGDKRLGIIGHMDVVPAGEGWTRDPFKMEIDEEGRIYGRGSADDKGPSLTAYYGMLLLKEAGFKPKKKIDFVLGTNEETNWVGIDYYLKHEPTPDIVFSPDAEYPIINGEQGIFTLEFSFKNDDTKGDYVLDKFKAGIATNVTPQVTRATISGPDLEAVKLAYESFLADKELDGSFEINDESADIVLIGQGAHASAPQVGKNSATFLALFLDQYAFAGRDKNFLHFLAEVEHEDFYGKKLGIFHHDDLMGDLASSPSMFDYEHAGKASLLNNVRYPQGTDPDTMIKQVLDKFSGILDVTYNGFEEPHYVPGSDPMVQTLLKVYEKQTGKPGHEVVIGGGTYGRLFERGVAFGAQPENGPMVMHAANEFMMLDDLILSIAIYAEAIYELTKDEEL

Source Source

Source organism organism	Lactobacillus delbrueckii
NCBI taxonomy ID ncbi_taxonomy_id	29397
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	2

Entity 3 Entity 3 non-polymer

Description description	3-[(1-AMINO-2-CARBOXY-ETHYL)-HYDROXY-PHOSPHINOYL]-2-METHYL-PROPIONIC ACID
Molecular weight formula_weight	239.2 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	570

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1lfwa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1lfwa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

CATH v4.4 (3 domains)

Domain ID domain_id	1lfwA01
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	1lfwA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

Domain ID domain_id	1lfwA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

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Unit-cell length a length_a	67.151 Å
Unit-cell length b length_b	77.025 Å
Unit-cell length c length_c	89.955 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	11.000 Å
R factor r_factor	—
R_work r_work	0.1743
R_free r_free	—

Crystal structure of pepV

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

pepV

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

1lfw__assembly_1__model_1

1lfw__assembly_1__model_1 | I(q)

1lfw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of pepV

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

pepV

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

1lfw__assembly_1__model_1

1lfw__assembly_1__model_1 | I(q)

1lfw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)