SAXSdb — 4w8f

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

Dynein heavy chain lysozyme chimera

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 1	Consistent with protein count
3	Insufficient information	Homooligomer	Protein 2	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 8 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENLYS_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1683–1842； UniProt 2–161 Author chain B； PDBConstruct 1683–1842； UniProt 2–161

Dynein heavy chain lysozyme chimera

Saccharomyces cerevisiae

UniProt P36022

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 1	Consistent with protein count
3	Insufficient information	Homooligomer	Protein 2	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 8 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DYHC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–1676； UniProt 1364–3038 Author chain A； PDBConstruct 1849–2649； UniProt 3292–4092 Author chain B； PDBConstruct 2–1676； UniProt 1364–3038 Author chain B； PDBConstruct 1849–2649； UniProt 3292–4092

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	4w8f
Deposition date deposition_date	2014-08-24
Structure title title	Crystal structure of the dynein motor domain in the AMPPNP-bound state
Keywords keywords	cytoplasmic dynein, microtubule, ATPase, AAA+, AMPPNP, MOTOR PROTEIN; MOTOR 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.

4w8f__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4w8f__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4w8f__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	63.44 Å
Rg (electron density)	63.65 Å
Total Rg	63.70 Å
Atom count	84822
Residues	5217
Excluded volume	759730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4w8f__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4w8f__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4w8f__assembly_3__model_1`	dimeric （2）	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	Dynein heavy chain lysozyme chimera
Molecular weight formula_weight	304889.9 kDa
EC 编号 ec_number	3.2.1.17
Mutation mutation	E1849Q
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	84822

GEFVIEKSLNRIKKFWKEAQYEVIEHSSGLKLVREWDVLEQACKEDLEELVSMKASNYYKIFEQDCLDLESKLTKLSEIQVNWVEVQFYWLDLYGILGENLDIQNFLPLETSKFKSLTSEYKMITTRAFQLDTTIEVIHIPNFDTTLKLTIDSLKMIKSSLSTFLERQRRQFPRFYFLGNDDLLKIIGSGKHHDQVSKFMKKMFGSIESIIFLEDFITGVRSVEGEVLNLNEKIELKDSIQAQEWLNILDTEIKLSVFTQFRDCLGQLKDGTDIEVVVSKYIFQAILLSAQVMWTELVEKCLQTNQFSKYWKEVDMKIKGLLDKLNKSSDNVKKKIEALLVEYLHFNNVIGQLKNCSTKEEARLLWAKVQKFYQKNDTLDDLNSVFISQSGYLLQYKFEYIGIPERLIYTPLLLIGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDQFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMKSPQSGTIAEMILQIMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNCSPLISEFGEGEKTVVESLKRVILPSLGDTDELVFKDELSKIFDSAGTPLNSKAIVQCLKDAGQRSGFSMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVIDAMAIFDGHANVVYVIDTKVLTKESLYGSMLKATLEWRDGLFTSILRRVNDDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDNKILTLPNGERLPIPPNFRILFETDNLDHTTPATITRCGLLWFSTDVCSISSKIDHLLNKSYEALDNKLSMFELDKLKDLISDSFDMASLTNIFTCSNDLVHILGVRTFNKLETAVQLAVHLISSYRQWFQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINTYFGHDSQELSDYSTIVIANDKLSFSSFCSEIPSVSLEAHEVMRPDIVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSLSQIYEIYYKAIFKLVPEFRSYTEPFARASVHLYNECKARYSTGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNSFEQLLYETVDKYLPNQDLGNISSTSLLFSGLLSLDFKEVNKTDLVNFIEERFKTFCDEELEVPMVIHESMVDHILRIDRALKQVQGHMMLIGASRTGKTILTRFVAWLNGLKIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDESNILETAFLERMNTLLANADIPDLFQGEEYDKLLNNLRNKTRSLGLLLDTEQELYDWFVGEIAKNLHVVFTICDPTNNKSSAMISSPALFNRCIINWMGDWDTKTMSQVANNMVDVIPMEFTDFIVPEVNKELVFTEPIQTIRDAVVNILIHFDRNFYQKMKVGVNPRSPGYFIDGLRALVKLVTAKYQDLQENQRFVNVGLEKLNESVLKVNELNKTLGSGSGSNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYGSGSGSSISLVKSLTFEKERWLNTTKQFSKTSQELIGNCIISSIYETYFGHLNERERADMLVILKRLLGKFAVKYDVNYRFIDYLVTLDEKMKWLECGLDKNDYFLENMSIVMNSQDAVPFLLDPSSHMITVISNYYGNKTVLLSFLEEGFVKRLENAIRFGSVVIIQDGEFFDPIISRLISREFNHAGNRVTVEIGDHEVDVSGDFKLFIHSCDPSGDIPIFLRSRVRLVHFVTNKESIETRIFDITLTEENAEMQRKREDLIKLNTEYKLKLKNLEKRLLEELNNSQGNMLENDELMVTLNNLKKEAMNIEKKLSESEEFFPQFDNLVEEYSIIGKHSVKIFSMLEKFGQFHWFYGISIGQFLSCFKRVFIKKSRETRAARTRVDEILWLLYQEVYCQFSTALDKKFKMIMAMTMFCLYKFDIESEQYKEAVLTMIGVLSESSDGVPKLTVDTNDDLRYLWDYVTTKSYISALNWFKNEFFVDEWNIADVVANSENNYFTMASERDVDGTFKLIELAKASKESLKIIPLGSIENLNYAQEEISKSKIEGGWILLQNIQMSLSWVKTYLHKHVEETKAAEEHEKFKMFMTCHLTGDKLPAPLLQRTDRVVYEDIPGILDTVKDLWGSQFFTGKISGVWSVYCTFLLSWFHALITARTRLVPHGFSKKYYFNDCDFQFASVYLENVLATNSTNNIPWAQVRDHIATIVYGGKIDEEKDLEVVAKLCAHVFCGSDNLQIVPGVRIPQPLLQQSEEEERARLTAILSNTIEPADSLSSWLQLPRESILDYERLQAKEVASSTEQLLQEMGSGSGSHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4w8fA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	100 — Dynein motor heavy chain, linker domain, N-terminal subdomain

Domain ID domain_id	4w8fA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	720 — Region D6 of dynein motor

Domain ID domain_id	4w8fB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	100 — Dynein motor heavy chain, linker domain, N-terminal subdomain

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Unit-cell length a length_a	137.730 Å
Unit-cell length b length_b	154.380 Å
Unit-cell length c length_c	177.550 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.59 °
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	3.541 Å
Low-resolution limit resolution_low	49.400 Å
R factor r_factor	0.2299
R_work r_work	0.2282
R_free r_free	0.2620

Crystal structure of the dynein motor domain in the AMPPNP-bound state

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

Dynein heavy chain lysozyme chimera

State in the Current Structure

Other States of the Same Protein in the Database

Dynein heavy chain lysozyme chimera

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

4w8f__assembly_3__model_1

4w8f__assembly_3__model_1 | I(q)

4w8f__assembly_3__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 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of the dynein motor domain in the AMPPNP-bound state

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

Dynein heavy chain lysozyme chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Dynein heavy chain lysozyme chimera

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

4w8f__assembly_3__model_1

4w8f__assembly_3__model_1 | I(q)

4w8f__assembly_3__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 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)