1v0f

Endosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid

Method: X-RAY DIFFRACTION

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

ENDO-ALPHA-SIALIDASE

COLIPHAGE K1F

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 3 其他Polymer 1	N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid × 1 N-acetyl-beta-neuraminic acid × 3 PHOSPHATE ION × 3 water × 3	Consistent with protein count
2	Other combination	Homooligomer	Protein 3 其他Polymer 2	N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid × 2 N-acetyl-beta-neuraminic acid × 3 PHOSPHATE ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q858B1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–666； UniProt 246–910 Author chain B； PDBConstruct 2–666； UniProt 246–910 Author chain C； PDBConstruct 2–666； UniProt 246–910 Author chain D； PDBConstruct 2–666； UniProt 246–910 Author chain E； PDBConstruct 2–666； UniProt 246–910 Author chain F； PDBConstruct 2–666； UniProt 246–910

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	1v0f
Deposition date deposition_date	2004-03-28
Structure title title	Endosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid
Keywords keywords	ENDOSIALIDASE, POLYSIALIC ACID DEGRADATION, HYDROLASE, GLYCOSIDASE.; 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.

1v0f__assembly_1__model_1

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

Download this curve (.dat)

1v0f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1v0f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.95 Å
Rg (electron density)	38.13 Å
Total Rg	38.62 Å
Atom count	15809
Residues	1998
Excluded volume	276550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1v0f__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1v0f__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	ENDO-ALPHA-SIALIDASE
Molecular weight formula_weight	74132.0 kDa
EC 编号 ec_number	3.2.1.129
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	32580

SAKGDGVTDDTAALTSALNDTPVGQKINGNGKTYKVTSLPDISRFINTRFVYERIPGQPLYYASEEFVQGELFKITDTPYYNAWPQDKAFVYENVIYAPYMGSDRHGVSRLHVSWVKSGDDGQTWSTPEWLTDLHPDYPTVNYHCMSMGVCRNRLFAMIETRTLAKNALTNCALWDRPMSRSLHLTGGITKAANQRYATIHVPDHGLFVGDFVNFSNSAVTGVSGDMTVATVIDKDNFTVLTPNQQTSDLNNAGKNWHMGTSFHKSPWRKTDLGLIPSVTEVHSFATIDNNGFAMGYHQGDVAPREVGLFYFPDAFNSPSNYVRRQIPSEYEPDASEPCIKYYDGVLYLITRGTRGDRLGSSLHRSRDIGQTWESLRFPHNVHHTTLPFAKVGDDLIMFGSERAENEWEAGAPDDRYKASYPRTFYARLNVNNWNADDIEWVNITDQIYQGGIVNSGVGVGSVVVKDNYIYYMFGGEDHFNPWTYGDNSAKDPFKSDGHPSDLYCYKMKIGPDNRVSRDFRYGAVPNRAVPVFFDTNGVRTVPAPMEFTGDLGLGHVTIRASTSSNIRSEVLMEGEYGFIGKSIPTDNPAGQRIIFCGGEGTSSTTGAQITLYGANNTDSRRIVYNGDEHLFQSADVKPYNDNVTALGGPSNRFTTAYLGSNPIVT

Source Source

Source organism organism	COLIPHAGE K1F
NCBI taxonomy ID ncbi_taxonomy_id	344021
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid
Molecular weight formula_weight	600.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	N-acetyl-beta-neuraminic acid
Molecular weight formula_weight	309.3 kDa
Source method src_method	man
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	921

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1v0fa1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.1 — Sialidases
Family Family family	b.68.1.2 — Endo-alpha-sialidase

Domain ID domain_id	d1v0fa2
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.108.1.3 — Endo-alpha-sialidase

Domain ID domain_id	d1v0fb1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.1 — Sialidases
Family Family family	b.68.1.2 — Endo-alpha-sialidase

Domain ID domain_id	d1v0fb2
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.108.1.3 — Endo-alpha-sialidase

Domain ID domain_id	d1v0fc1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.1 — Sialidases
Family Family family	b.68.1.2 — Endo-alpha-sialidase

Domain ID domain_id	d1v0fc2
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.108.1.3 — Endo-alpha-sialidase

Domain ID domain_id	d1v0fd1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.1 — Sialidases
Family Family family	b.68.1.2 — Endo-alpha-sialidase

Domain ID domain_id	d1v0fd2
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.108.1.3 — Endo-alpha-sialidase

Domain ID domain_id	d1v0fe1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.1 — Sialidases
Family Family family	b.68.1.2 — Endo-alpha-sialidase

Domain ID domain_id	d1v0fe2
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.108.1.3 — Endo-alpha-sialidase

Domain ID domain_id	d1v0ff1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.1 — Sialidases
Family Family family	b.68.1.2 — Endo-alpha-sialidase

Domain ID domain_id	d1v0ff2
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.108.1.3 — Endo-alpha-sialidase

CATH v4.4 (24 domains)

Domain ID domain_id	1v0fA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

Domain ID domain_id	1v0fA02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1v0fA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1v0fA04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1090 — Endosialidase, domain 4
Homologous superfamily homologous superfamily	10 — Endosialidase, domain 4

Domain ID domain_id	1v0fB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

Domain ID domain_id	1v0fB02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1v0fB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1v0fB04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1090 — Endosialidase, domain 4
Homologous superfamily homologous superfamily	10 — Endosialidase, domain 4

Domain ID domain_id	1v0fC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

Domain ID domain_id	1v0fC02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1v0fC03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1v0fC04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1090 — Endosialidase, domain 4
Homologous superfamily homologous superfamily	10 — Endosialidase, domain 4

Domain ID domain_id	1v0fD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

Domain ID domain_id	1v0fD02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1v0fD03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1v0fD04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1090 — Endosialidase, domain 4
Homologous superfamily homologous superfamily	10 — Endosialidase, domain 4

Domain ID domain_id	1v0fE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

Domain ID domain_id	1v0fE02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1v0fE03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1v0fE04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1090 — Endosialidase, domain 4
Homologous superfamily homologous superfamily	10 — Endosialidase, domain 4

Domain ID domain_id	1v0fF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

Domain ID domain_id	1v0fF02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1v0fF03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1v0fF04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1090 — Endosialidase, domain 4
Homologous superfamily homologous superfamily	10 — Endosialidase, domain 4

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Unit-cell length a length_a	99.540 Å
Unit-cell length b length_b	131.400 Å
Unit-cell length c length_c	346.040 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	24

Space group space_group	P 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1826
R_work r_work	0.1800
R_free r_free	0.2315

Endosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid

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

ENDO-ALPHA-SIALIDASE

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

1v0f__assembly_1__model_1

1v0f__assembly_1__model_1 | I(q)

1v0f__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (2)

Endosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid

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

ENDO-ALPHA-SIALIDASE

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

1v0f__assembly_1__model_1

1v0f__assembly_1__model_1 | I(q)

1v0f__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (2)