4m4u

Structural evaluation D84A mutant of the aspergillus fumigatus kdnase (sialidase)

Method: X-RAY DIFFRACTION

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

Extracellular sialidase/neuraminidase, putative

Aspergillus fumigatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 GLYCEROL × 4 PHOSPHATE ION × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GLYCEROL × 3 PHOSPHATE ION × 1 NITRATE ION × 2 NITRITE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4WQS0_ASPFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–422； UniProt 1–406 Author chain B； PDBConstruct 17–422； UniProt 1–406

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	4m4u
Deposition date deposition_date	2013-08-07
Structure title title	Structural evaluation D84A mutant of the aspergillus fumigatus kdnase (sialidase)
Keywords keywords	KDNase, HYDROLASE; 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.

4m4u__assembly_1__model_1

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

Download this curve (.dat)

4m4u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4m4u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.42 Å
Rg (electron density)	19.34 Å
Total Rg	20.23 Å
Atom count	2983
Residues	384
Excluded volume	52206 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4m4u__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4m4u__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Description description	Extracellular sialidase/neuraminidase, putative
Molecular weight formula_weight	46232.6 kDa
EC 编号 ec_number	3.2.1.18
Mutation mutation	D84A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7205

HHHHHHSSGLVPRGSHMQSMRFMILALLVQFLPAWAINDPAKSAAPYHDEFPLFRSANMASPDKLSTGIGFHSFRIPAVVRTTTGRILAFAEGRRHTNQAFGDINLVYKRTKTTANNGASPSDWEPLREVVGSGAGTWGNPTPVVDDDNTIYLFLSWNGATYSQNGKDVLPDGTVTKKIDSTWEGRRHLYLTESRDDGNTWSKPVDLTKELTPDGWAWDAVGPGNGIRLTTGELVIPAMGRNIIGRGAPGNRTWSVQRLSGAGAEGTIVQTPDGKLYRNDRPSQKGYRMVARGTLEGFGAFAPDAGLPDPACQGSVLRYNSDAPARTIFLNSASGTSRRAMRVRISYDADAKKFNYGRKLEDAKVSGAGHEGGYSSMTKTGDYKIGALVESDFFNDGTGKNSYRAIIWRRFNLSWILNGPNN

Source Source

Source organism organism	Aspergillus fumigatus
NCBI taxonomy ID ncbi_taxonomy_id	330879
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

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	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	NITRITE ION
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1162

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4m4uA00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4m4uB00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	75.940 Å
Unit-cell length b length_b	57.870 Å
Unit-cell length c length_c	94.610 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.840 Å
Low-resolution limit resolution_low	12.390 Å
R factor r_factor	0.1446
R_work r_work	0.1428
R_free r_free	0.1789

Structural evaluation D84A mutant of the aspergillus fumigatus kdnase (sialidase)

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

Extracellular sialidase/neuraminidase, putative

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

4m4u__assembly_1__model_1

4m4u__assembly_1__model_1 | I(q)

4m4u__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structural evaluation D84A mutant of the aspergillus fumigatus kdnase (sialidase)

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

Extracellular sialidase/neuraminidase, putative

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

4m4u__assembly_1__model_1

4m4u__assembly_1__model_1 | I(q)

4m4u__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)