SAXSdb — 1c5e

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

HEAD DECORATION PROTEIN

Enterobacteria phage lambda

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	GLYCEROL × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VCAD_LAMBD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 16–110 Author chain B； PDBConstruct 1–95； UniProt 16–110 Author chain C； PDBConstruct 1–95； UniProt 16–110

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	1c5e
Deposition date deposition_date	1999-11-18
Structure title title	BACTERIOPHAGE LAMBDA HEAD PROTEIN D
Keywords keywords	BACTERIOPHAGE LAMBDA, HEAD PROTEIN D, PROTEIN CRYSTAL STRUCTURE, VIRUS ASSEMBLY, PHAGE DISPLAY, 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.

1c5e__assembly_1__model_1

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

Download this curve (.dat)

1c5e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1c5e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.49 Å
Rg (electron density)	18.41 Å
Total Rg	19.48 Å
Atom count	2085
Residues	285
Excluded volume	37080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1c5e__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	HEAD DECORATION PROTEIN
Molecular weight formula_weight	9830.0 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	2409

SDPAHTATAPGGLSAKAPAMTPLMLDTSSRKLVAWDGTTDGAAVGILAVAADQTSTTLTFYKSGTFRYEDVLWPEAASDETKKRTAFAGTAISIV

Source Source

Source organism organism	Enterobacteria phage lambda
NCBI taxonomy ID ncbi_taxonomy_id	10710

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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	309

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1c5ea_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.2 — Head decoration protein D (gpD, major capsid protein D)
Family Family family	b.85.2.1 — Head decoration protein D (gpD, major capsid protein D)

Domain ID domain_id	d1c5eb_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.2 — Head decoration protein D (gpD, major capsid protein D)
Family Family family	b.85.2.1 — Head decoration protein D (gpD, major capsid protein D)

Domain ID domain_id	d1c5ec_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.2 — Head decoration protein D (gpD, major capsid protein D)
Family Family family	b.85.2.1 — Head decoration protein D (gpD, major capsid protein D)

CATH v4.4 (3 domains)

Domain ID domain_id	1c5eA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	1c5eB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	1c5eC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

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Unit-cell length a length_a	45.580 Å
Unit-cell length b length_b	69.070 Å
Unit-cell length c length_c	45.590 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.0986
R_work r_work	—
R_free r_free	0.1328

BACTERIOPHAGE LAMBDA HEAD PROTEIN D

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

HEAD DECORATION 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

1c5e__assembly_1__model_1

1c5e__assembly_1__model_1 | I(q)

1c5e__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

BACTERIOPHAGE LAMBDA HEAD PROTEIN D

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

HEAD DECORATION 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

1c5e__assembly_1__model_1

1c5e__assembly_1__model_1 | I(q)

1c5e__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)