2bse

Structure of Lactococcal Bacteriophage p2 Receptor Binding Protein in complex with a llama VHH domain

Method: X-RAY DIFFRACTION

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

RECEPTOR BINDING PROTEIN

LACTOCOCCUS VIRUS P2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	LLAMA IMMUNOGLOBULIN × 3 water × 1	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	2bse
Deposition date deposition_date	2005-05-20
Structure title title	Structure of Lactococcal Bacteriophage p2 Receptor Binding Protein in complex with a llama VHH domain
Keywords keywords	LACTOCOCCUS LACTIS, PHAGE, RECEPTOR BINDING PROTEIN, LLAMA ANTIBODY, VHH, RECEPTOR; RECEPTOR
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.

2bse__assembly_1__model_1

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

Download this curve (.dat)

2bse__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bse__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.25 Å
Rg (electron density)	29.59 Å
Total Rg	30.32 Å
Atom count	5310
Residues	687
Excluded volume	93421 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bse__assembly_1__model_1`	hexameric （6）	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	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	5311

MTIKNFTFFSPNSTEFPVGSNNDGKLYMMLTGMDYRTIRRKDWSSPLNTALNVQYTNTSIIAGGRYFELLNETVALKGDSVNYIHANIDLTQTANPVSLSAETANNSNGVDINNGSGVLKVCFDIVTTSGTGVTSTKPIVQTSTLDSISVNDMTVSGSIDVPVQTLTVEAGNGLQLQLTKKNNDLVIVRFFGSVSNIQKGWNMSGTWVDRPFRPAAVQSLVGHFAGRDTSFHIDINPNGSITWWGANIDKTPIATRGNGSYFIK

Source Source

Source organism organism	LACTOCOCCUS VIRUS P2
NCBI taxonomy ID ncbi_taxonomy_id	254252
Host organism host_organism	ESCHERICHIA COLI K-12

Entity 2 Entity 2 polymer

Description description	LLAMA IMMUNOGLOBULIN
Molecular weight formula_weight	13499.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

QVQLQESGGGLVQAGGSLRLSCTASRRTGSNWCMGWFRQLAGKEPELVVALNFDYDMTYYADSVKGRFTVSRDSGKNTVYLQMNSLKPEDTAIYYCAARSGGFSSNRELYDGWGQGTQVTVSS

Source Source

Source organism organism	LAMA GLAMA
Common name common_name	LLAMA
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	SACCHAROMYCES CEREVISIAE

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2bsea_
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	d2bseb_
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	d2bsec_
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	d2bsed1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2bsed2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2bsee1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2bsee2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2bsef1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2bsef2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	2bseA00
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	2bseB00
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	2bseC00
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	2bseD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2bseE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2bseF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	74.763 Å
Unit-cell length b length_b	83.939 Å
Unit-cell length c length_c	137.793 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	2.700 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2530
R_work r_work	0.2510
R_free r_free	0.2940

Structure of Lactococcal Bacteriophage p2 Receptor Binding Protein in complex with a llama VHH domain

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

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

2bse__assembly_1__model_1

2bse__assembly_1__model_1 | I(q)

2bse__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 polymer

Polymer Polymer

Source Source

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 Lactococcal Bacteriophage p2 Receptor Binding Protein in complex with a llama VHH domain

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

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

2bse__assembly_1__model_1

2bse__assembly_1__model_1 | I(q)

2bse__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 polymer

Polymer Polymer

Source Source

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)