5dn6

ATP synthase from Paracoccus denitrificans

Method: X-RAY DIFFRACTION

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

ATP synthase subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Chain A × 1 Chain B × 1 Chain C × 1 ATP synthase subunit beta × 3 （A1B8P0） ATP synthase gamma chain × 1 （A1B8N9） ATP synthase subunit delta × 1 （A1B8N7） ATP synthase epsilon chain × 1 （A1B8P1） ATP synthase F0 subcomplex C subunit × 12 （A1B618） Chain V × 1 Chain W × 1 ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a × 1 （A1B619） Chain Y × 1 Zeta inhibitor protein × 1 （A1B602） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPA_PARDP
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–511； UniProt 1–511 Author chain B； PDBConstruct 1–511； UniProt 1–511 Author chain C； PDBConstruct 1–511； UniProt 1–511

ATP synthase subunit beta

OrganismNot specified

UniProt A1B8P0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Chain A × 1 Chain B × 1 Chain C × 1 ATP synthase subunit alpha × 3 （A1B8N8） ATP synthase gamma chain × 1 （A1B8N9） ATP synthase subunit delta × 1 （A1B8N7） ATP synthase epsilon chain × 1 （A1B8P1） ATP synthase F0 subcomplex C subunit × 12 （A1B618） Chain V × 1 Chain W × 1 ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a × 1 （A1B619） Chain Y × 1 Zeta inhibitor protein × 1 （A1B602） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPB_PARDP
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain D； PDBConstruct 1–474； UniProt 1–474 Author chain E； PDBConstruct 1–474； UniProt 1–474 Author chain F； PDBConstruct 1–474； UniProt 1–474

ATP synthase gamma chain

OrganismNot specified

UniProt A1B8N9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Chain A × 1 Chain B × 1 Chain C × 1 ATP synthase subunit alpha × 3 （A1B8N8） ATP synthase subunit beta × 3 （A1B8P0） ATP synthase subunit delta × 1 （A1B8N7） ATP synthase epsilon chain × 1 （A1B8P1） ATP synthase F0 subcomplex C subunit × 12 （A1B618） Chain V × 1 Chain W × 1 ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a × 1 （A1B619） Chain Y × 1 Zeta inhibitor protein × 1 （A1B602） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPG_PARDP
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–290； UniProt 1–290

ATP synthase subunit delta

OrganismNot specified

UniProt A1B8N7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Chain A × 1 Chain B × 1 Chain C × 1 ATP synthase subunit alpha × 3 （A1B8N8） ATP synthase subunit beta × 3 （A1B8P0） ATP synthase gamma chain × 1 （A1B8N9） ATP synthase epsilon chain × 1 （A1B8P1） ATP synthase F0 subcomplex C subunit × 12 （A1B618） Chain V × 1 Chain W × 1 ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a × 1 （A1B619） Chain Y × 1 Zeta inhibitor protein × 1 （A1B602） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPD_PARDP
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain H； PDBConstruct 1–188； UniProt 1–188

ATP synthase epsilon chain

OrganismNot specified

UniProt A1B8P1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Chain A × 1 Chain B × 1 Chain C × 1 ATP synthase subunit alpha × 3 （A1B8N8） ATP synthase subunit beta × 3 （A1B8P0） ATP synthase gamma chain × 1 （A1B8N9） ATP synthase subunit delta × 1 （A1B8N7） ATP synthase F0 subcomplex C subunit × 12 （A1B618） Chain V × 1 Chain W × 1 ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a × 1 （A1B619） Chain Y × 1 Zeta inhibitor protein × 1 （A1B602） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPE_PARDP
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain I； PDBConstruct 1–148； UniProt 1–148

ATP synthase F0 subcomplex C subunit

OrganismNot specified

UniProt A1B618

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Chain A × 1 Chain B × 1 Chain C × 1 ATP synthase subunit alpha × 3 （A1B8N8） ATP synthase subunit beta × 3 （A1B8P0） ATP synthase gamma chain × 1 （A1B8N9） ATP synthase subunit delta × 1 （A1B8N7） ATP synthase epsilon chain × 1 （A1B8P1） Chain V × 1 Chain W × 1 ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a × 1 （A1B619） Chain Y × 1 Zeta inhibitor protein × 1 （A1B602） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A1B618_PARDP
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain J； PDBConstruct 1–77； UniProt 1–77 Author chain K； PDBConstruct 1–77； UniProt 1–77 Author chain L； PDBConstruct 1–77； UniProt 1–77 Author chain M； PDBConstruct 1–77； UniProt 1–77 Author chain N； PDBConstruct 1–77； UniProt 1–77 Author chain O； PDBConstruct 1–77； UniProt 1–77 Author chain P； PDBConstruct 1–77； UniProt 1–77 Author chain Q； PDBConstruct 1–77； UniProt 1–77 Author chain R； PDBConstruct 1–77； UniProt 1–77 Author chain S； PDBConstruct 1–77； UniProt 1–77 Author chain T； PDBConstruct 1–77； UniProt 1–77 Author chain U； PDBConstruct 1–77； UniProt 1–77

ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a

OrganismNot specified

UniProt A1B619

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Chain A × 1 Chain B × 1 Chain C × 1 ATP synthase subunit alpha × 3 （A1B8N8） ATP synthase subunit beta × 3 （A1B8P0） ATP synthase gamma chain × 1 （A1B8N9） ATP synthase subunit delta × 1 （A1B8N7） ATP synthase epsilon chain × 1 （A1B8P1） ATP synthase F0 subcomplex C subunit × 12 （A1B618） Chain V × 1 Chain W × 1 Chain Y × 1 Zeta inhibitor protein × 1 （A1B602） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATP6_PARDP
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain X； PDBConstruct 36–283； UniProt 1–248

Zeta inhibitor protein

OrganismNot specified

UniProt A1B602

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Chain A × 1 Chain B × 1 Chain C × 1 ATP synthase subunit alpha × 3 （A1B8N8） ATP synthase subunit beta × 3 （A1B8P0） ATP synthase gamma chain × 1 （A1B8N9） ATP synthase subunit delta × 1 （A1B8N7） ATP synthase epsilon chain × 1 （A1B8P1） ATP synthase F0 subcomplex C subunit × 12 （A1B618） Chain V × 1 Chain W × 1 ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a × 1 （A1B619） Chain Y × 1 ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A1B602_PARDP
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain Z； PDBConstruct 1–104； UniProt 1–104

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	5dn6
Deposition date deposition_date	2015-09-09
Structure title title	ATP synthase from Paracoccus denitrificans
Keywords keywords	Hydrolase, Paracoccus denitrificans, ATP synthase, complex, regulation, proton translocation; 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.

5dn6__assembly_1__model_1

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

Download this curve (.dat)

5dn6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dn6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.93 Å
Rg (electron density)	59.75 Å
Total Rg	58.97 Å
Atom count	31527
Residues	4682
Excluded volume	550460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dn6__assembly_1__model_1`	29-meric （29）	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 (17)

Entity 1 Entity 1 polymer

Description description	Chain A
Molecular weight formula_weight	1720.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1
Atom count atom_count	31527

XXXXXXXXXXXXXXXXXXXX

Entity 2 Entity 2 polymer

Description description	Chain B
Molecular weight formula_weight	1294.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

XXXXXXXXXXXXXXX

Entity 3 Entity 3 polymer

Description description	Chain C
Molecular weight formula_weight	1635.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

XXXXXXXXXXXXXXXXXXX

Entity 4 Entity 4 polymer

Description description	ATP synthase subunit alpha
Molecular weight formula_weight	55099.8 kDa
EC 编号 ec_number	7.1.2.2
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

MGIQAAEISAILKDQIKNFGQDAEVAEVGQVLSVGDGIARVYGLDKVQAGEMVEFPGGIRGMVLNLETDNVGVVIFGDDRDIKEGDTVKRTGAIVEVPAGKELLGRVVDALGNPIDGKGPLNASERRIADVKAPGIMPRKSVHEPMATGLKSVDAMIPVGRGQRELIIGDRQTGKTAIALDTILNQANYNGREADGMKTLHCIYVAVGQKRSTVAQLVKKLEETGAMAYTTVVAATASDPAPMQYLAPYSATAMGEYFRDNGMDALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERSAKLNEANGAGSLTALPIIETQAGDVSAYIPTNVISITDGQIFLETELFFQGIRPAVNTGLSVSRVGSAAQTKAMKSVAGPVKLELAQYREMAAFAQFGSDLDAATQKLLNRGARLTELMKQPQYSPLTNAEIVIVIYAGTKGYLDGIPVRDVTKWEHGLLQYLRNQKADLLEDMTKNDRKVAGELEDAIKAALDGYAKTYA

Entity 5 Entity 5 polymer

Description description	ATP synthase subunit beta
Molecular weight formula_weight	50386.0 kDa
EC 编号 ec_number	7.1.2.2
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MAEANGKITQVIGAVVDVQFDGQLPAILNALETENNGKRLVLEVAQHLGENTVRTIAMDATEGLVRGLPVKDTGGPIMVPVGDATLGRILNVVGEPVDEGGPVEATQTRAIHQQAPDFAAQATASEILVTGIKVIDLLAPYSKGGKIGLFGGAGVGKTVLIMELINNIAKVHSGYSVFAGVGERTREGNDLYHEMVESGVIKPDDLSKSQVALVYGQMNEPPGARMRVALTGLTVAEQFRDATGTDVLFFVDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGAMQERITSTKNGSITSIQAVYVPADDLTDPAPATTFAHLDATTVLSRAISELGIYPAVDPLDSNSRILDPAVVGEEHYQVARDVQGILQKYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFDVAKVFTGSDGVQVPLEDTIKSFKAVVAGEYDHLPEAAFYMVGGIEDVKAKAQRLAADAA

Entity 6 Entity 6 polymer

Description description	ATP synthase gamma chain
Molecular weight formula_weight	31639.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MPSLKDLKNRIGSVKNTRKITKAMQMVAAAKLRRAQEAAEAARPYADRMAAVMAGLTAAAAGSDMAPRLLAGTGEDRRHLLVVMTSERGLAGGFNSSIVKLARLRLQELQAQGKQVSILTVGKKGREQLKREYGDLFVNHVDLSEVKRIGYDNARAIADEILDRFDNGEFDVATLFYNRFESVISQVPTARQVIPAVIEEGEAGASSLYDYEPDENAILNDLLPRSVATQVFAALLENAASEQGARMTAMDNATRNAGDMIDRLTTVYNRSRQAAITKELIEIISGAEAL

Entity 7 Entity 7 polymer

Description description	ATP synthase subunit delta
Molecular weight formula_weight	20047.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MTVANSASISADIAGRYAQALFDLVRDSGGIDALSSQIDDLASAYDASQDLRDLTLSPLYDRQQQEAAVGALSERMGLSAELANTLRLLARNRRLFTLPQFVAKLRNLIADAKGEVTADVVSAQALTDEQKARLADTLAAKSGKTVKLNARVDESLIGGMIVKLGSQMIDSSIRSKLASLQNAMKEVG

Entity 8 Entity 8 polymer

Description description	ATP synthase epsilon chain
Molecular weight formula_weight	15840.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MADTMQFDLVSPERNLVSVPVREVRLPGADGDLTAMPGHAPAIVNLRPGLVTVVAGDGSETEFAVTGGFAEINNESVTLLAERGHPRAEMTQEVFNEMMAQARRRVEAAKERESAGEELVAAAVKLLADMEALGTHIGLDPNHANFPH

Entity 9 Entity 9 polymer

Description description	ATP synthase F0 subcomplex C subunit
Molecular weight formula_weight	7610.9 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K,L,M,N,O,P,Q,R,S,T,U

MENLGQLGQYLGAGLACVGMAGAAMGVGNVAGNYLAGALRNPSAAASQTATLFIGMAFAEALGIFSFLVALLLLFAV

Entity 10 Entity 10 polymer

Description description	Chain V
Molecular weight formula_weight	6656.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 11 Entity 11 polymer

Description description	Chain W
Molecular weight formula_weight	10571.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 12 Entity 12 polymer

Description description	ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a
Molecular weight formula_weight	29724.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMAEEEAGGLVFHPMDQFVIKPLFGEGPVNWYTPTNATLWMALAALAITALLVFGTRGRAIVPNRVQSIAELLYGMVHKMVEDVTGKDGLKYFPYVMTLFCFILFANFLGLLPKSFSPTSHIAVTAVLAVLVFAGVTVLGFVKNGAHFLGLFWVSSAPLALRPVLAVIELISYFVRPVSHSIRLAGNIMAGHAVIKVFAAFAAVAAIAPVSVVAITAMYGLEVLVCLIQAYVFTILTCVYLKDALHPAH

Entity 13 Entity 13 polymer

Description description	Chain Y
Molecular weight formula_weight	4613.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 14 Entity 14 polymer

Description description	Zeta inhibitor protein
Molecular weight formula_weight	11687.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

MTTFDDRERAHEAKFAHDAELNFKAEARRNRLLGEWAAGLLGKTGDDARAYALTVVTSDFDEPGDEDVFRKLAADLEGKADEETIRAKMVELRATAREQIISEI

Entity 15 Entity 15 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 16 Entity 16 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 17 Entity 17 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 33 domains

CATH v4.4 (33 domains)

Domain ID domain_id	5dn6A01
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	5dn6A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5dn6A03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	20 — ATP synthase alpha/beta chain, C-terminal domain

Domain ID domain_id	5dn6B01
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	5dn6B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5dn6B03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	20 — ATP synthase alpha/beta chain, C-terminal domain

Domain ID domain_id	5dn6C01
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	5dn6C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5dn6C03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	20 — ATP synthase alpha/beta chain, C-terminal domain

Domain ID domain_id	5dn6D01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	5dn6D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5dn6D03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	5dn6E01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	5dn6E02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5dn6E03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	5dn6F01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	5dn6F02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5dn6F03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	5dn6G01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	80 — ATP synthase, gamma subunit, helix hairpin domain

Domain ID domain_id	5dn6G02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — ATP synthase, F1 complex, gamma subunit

Domain ID domain_id	5dn6I00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	15 — ATP Synthase; domain 1
Homologous superfamily homologous superfamily	10 — F0F1 ATP synthase delta/epsilon subunit, N-terminal

Domain ID domain_id	5dn6J00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6K00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6L00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6M00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6N00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6O00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6P00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6Q00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6R00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6S00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6T00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5dn6U00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

▶

Unit-cell length a length_a	112.001 Å
Unit-cell length b length_b	187.943 Å
Unit-cell length c length_c	164.724 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	3.980 Å
Low-resolution limit resolution_low	36.840 Å
R factor r_factor	0.2969
R_work r_work	0.2955
R_free r_free	0.3241

ATP synthase from Paracoccus denitrificans

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

ATP synthase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase gamma chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase subunit delta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase epsilon chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase F0 subcomplex C subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Zeta inhibitor 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

5dn6__assembly_1__model_1

5dn6__assembly_1__model_1 | I(q)

5dn6__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 (17)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer