1zru

structure of the lactophage p2 receptor binding protein in complex with glycerol

Method: X-RAY DIFFRACTION

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

lactophage p2 receptor binding protein

Lactococcus lactis phage p2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	GLYCEROL × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q71AW2_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–264； UniProt 1–264 Author chain B； PDBConstruct 1–264； UniProt 1–264 Author chain C； PDBConstruct 1–264； UniProt 1–264

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	1zru
Deposition date deposition_date	2005-05-22
Structure title title	structure of the lactophage p2 receptor binding protein in complex with glycerol
Keywords keywords	3 domains: BETA BARREL, BETA PRISM, BETA BARREL, Structural Genomics, Structural Proteomics in Europe, SPINE, VIRAL PROTEIN; VIRAL PROTEIN
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.

1zru__assembly_1__model_1

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

Download this curve (.dat)

1zru__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zru__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.11 Å
Rg (electron density)	31.27 Å
Total Rg	31.76 Å
Atom count	5816
Residues	758
Excluded volume	102930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zru__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	lactophage p2 receptor binding protein
Molecular weight formula_weight	28668.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6960

MTIKNFTFFSPNSTEFPVGSNNDGKLYMMLTGMDYRTIRRKDWSSPLNTALNVQYTNTSIIAGGRYFELLNETVALKGDSVNYIHANIDLTQTANPVSLSAETANNSNGVDINNGSGVLKVCFDIVTTSGTGVTSTKPIVQTSTLDSISVNDMTVSGSIDVPVQTLTVEAGNGLQLQLTKKNNDLVIVRFFGSVSNIQKGWNMSGTWVDRPFRPAAVQSLVGHFAGRDTSFHIDINPNGSITWWGANIDKTPIATRGNGSYFIK

Source Source

Source organism organism	Lactococcus lactis phage p2
NCBI taxonomy ID ncbi_taxonomy_id	100641
Host organism host_organism	Escherichia coli K12

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1144

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1zrua1
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.3 — Lactophage receptor-binding protein head domain

Domain ID domain_id	d1zrua2
Class class	b — All beta proteins
Fold Fold fold	b.108 — Triple-stranded beta-helix
Superfamily Superfamily superfamily	b.108.1 — Phage fibre proteins
Family Family family	b.108.1.4 — Lactophage receptor-binding protein domain

Domain ID domain_id	d1zrua3
Class class	b — All beta proteins
Fold Fold fold	b.163 — Pseudo beta-prism I
Superfamily Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
Family Family family	b.163.1.2 — Lactophage receptor-binding protein N-terminal domain

Domain ID domain_id	d1zrub1
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.3 — Lactophage receptor-binding protein head domain

Domain ID domain_id	d1zrub2
Class class	b — All beta proteins
Fold Fold fold	b.108 — Triple-stranded beta-helix
Superfamily Superfamily superfamily	b.108.1 — Phage fibre proteins
Family Family family	b.108.1.4 — Lactophage receptor-binding protein domain

Domain ID domain_id	d1zrub3
Class class	b — All beta proteins
Fold Fold fold	b.163 — Pseudo beta-prism I
Superfamily Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
Family Family family	b.163.1.2 — Lactophage receptor-binding protein N-terminal domain

Domain ID domain_id	d1zruc1
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.3 — Lactophage receptor-binding protein head domain

Domain ID domain_id	d1zruc2
Class class	b — All beta proteins
Fold Fold fold	b.108 — Triple-stranded beta-helix
Superfamily Superfamily superfamily	b.108.1 — Phage fibre proteins
Family Family family	b.108.1.4 — Lactophage receptor-binding protein domain

Domain ID domain_id	d1zruc3
Class class	b — All beta proteins
Fold Fold fold	b.163 — Pseudo beta-prism I
Superfamily Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
Family Family family	b.163.1.2 — Lactophage receptor-binding protein N-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1zruA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	520 — Triple-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Phage fibre proteins

Domain ID domain_id	1zruA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1830 — Phage tail base-plate Siphoviridae RBP, head domain

Domain ID domain_id	1zruB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	520 — Triple-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Phage fibre proteins

Domain ID domain_id	1zruB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1830 — Phage tail base-plate Siphoviridae RBP, head domain

Domain ID domain_id	1zruC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	520 — Triple-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Phage fibre proteins

Domain ID domain_id	1zruC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1830 — Phage tail base-plate Siphoviridae RBP, head domain

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Unit-cell length a length_a	81.106 Å
Unit-cell length b length_b	92.057 Å
Unit-cell length c length_c	145.725 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	12

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

Resolution resolution	1.730 Å
Low-resolution limit resolution_low	40.560 Å
R factor r_factor	0.1755
R_work r_work	0.1753
R_free r_free	0.1969

structure of the lactophage p2 receptor binding protein in complex with glycerol

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

lactophage p2 receptor binding protein

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

1zru__assembly_1__model_1

1zru__assembly_1__model_1 | I(q)

1zru__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)

structure of the lactophage p2 receptor binding protein in complex with glycerol

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

lactophage p2 receptor binding protein

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

1zru__assembly_1__model_1

1zru__assembly_1__model_1 | I(q)

1zru__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)