2vpy

Polysulfide reductase with bound quinone inhibitor, pentachlorophenol (PCP)

Method: X-RAY DIFFRACTION

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

THIOSULFATE REDUCTASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	NRFC PROTEIN × 2 （Q72LA5） HYPOTHETICAL MEMBRANE SPANNING PROTEIN × 2 （Q72LA6） IRON/SULFUR CLUSTER × 10 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 4 MOLYBDENUM ATOM × 2 PENTACHLOROPHENOL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72LA4_THET2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–765； UniProt 1–765 Author chain E； PDBConstruct 1–765； UniProt 1–765

NRFC PROTEIN

OrganismNot specified

UniProt Q72LA5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	THIOSULFATE REDUCTASE × 2 （Q72LA4） HYPOTHETICAL MEMBRANE SPANNING PROTEIN × 2 （Q72LA6） IRON/SULFUR CLUSTER × 10 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 4 MOLYBDENUM ATOM × 2 PENTACHLOROPHENOL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72LA5_THET2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–195； UniProt 1–195 Author chain F； PDBConstruct 1–195； UniProt 1–195

HYPOTHETICAL MEMBRANE SPANNING PROTEIN

OrganismNot specified

UniProt Q72LA6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	THIOSULFATE REDUCTASE × 2 （Q72LA4） NRFC PROTEIN × 2 （Q72LA5） IRON/SULFUR CLUSTER × 10 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 4 MOLYBDENUM ATOM × 2 PENTACHLOROPHENOL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72LA6_THET2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–253； UniProt 1–253 Author chain G； PDBConstruct 1–253； UniProt 1–253

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	2vpy
Deposition date deposition_date	2008-03-09
Structure title title	Polysulfide reductase with bound quinone inhibitor, pentachlorophenol (PCP)
Keywords keywords	;OXIDOREDUCTASE, MOLYBDOPTERIN GUANINE DINUCLEOTIDE, IRON-SULFUR, METAL-BINDING, MOLYBDOPTERIN, INTEGRAL MEMBRANE PROTEIN, MGD, MPT, IRON, FE4S4, 4FE-4S, MOLYBDENUM, IRON SULFUR CLUSTER ;; OXIDOREDUCTASE
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.

2vpy__assembly_1__model_1

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

Download this curve (.dat)

2vpy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vpy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.91 Å
Rg (electron density)	45.39 Å
Total Rg	45.06 Å
Atom count	18932
Residues	2360
Excluded volume	339600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vpy__assembly_1__model_1`	hexameric （6）	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	THIOSULFATE REDUCTASE
Molecular weight formula_weight	86737.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	20217

MQRREFLKLSALGVGAMALRGSGPAKALKAPWYAQEVKSVYQICEGCFWRCGIVAHAVGNRVYKVEGYEANPKSRGRLCPRGQGAPQTTYDPDRLKRPLIRVEGSQRGEGKYRVATWEEALDHIAKKMLEIREKYGPEAIAFFGHGTGDYWFVDFLPAAWGSPNAAKPSVSLCTAPREVASQWVFGRPIGGHEPIDWENARYIVLIGHHIGEDTHNTQLQDFALALKNGAKVVVVDPRFSTAAAKAHRWLPIKPGTDTALLLAWIHVLIYEDLYDKEYVAKYTVGFEELKAHVKDFTPEWAEKHTEIPAQVIREVAREMAAHKPRAVLPPTRHNVWYGDDTYRVMALLYVNVLLGNYGRPGGFYIAQSPYLEKYPLPPLPLEPAAGGCSGPSGGDHEPEGFKPRADKGKFFARSTAIQELIEPMITGEPYPIKGLFAYGINLFHSIPNVPRTKEALKNLDLYVAIDVLPQEHVMWADVILPEATYLERYDDFVLVAHKTPFIQLRTPAHEPLFDTKPGWWIARELGLRLGLEQYFPWKTIEEYLETRLQSLGLDLETMKGMGTLVQRGKPWLEDWEKEGRLPFGTASGKIELYCQRFKEAGHQPLPVFTPPEEPPEGFYRLLYGRSPVHTFARTQNNWVLMEMDPENEVWIHKEEAKRLGLKEGDYVMLVNQDGVKEGPVRVKPTARIRKDCVYIVHGFGHKAPLMRLAHGRGASDNYLQTRYKLDPISGGAGLRVNFVRLEKAERPRLPSLTGLAKRPFDERRM

Entity 2 Entity 2 polymer

Description description	NRFC PROTEIN
Molecular weight formula_weight	21405.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MPRYAMAIDLSLCVGCAACAVACKMENEVPPGVFNLWIREREVGEYPNLVVEFRPEQCLHCENPPCVPVCPTGASYQTKDGLVLVDPKKCIACGACIAACPYDARYLHPAGYVSKCTFCAHRLEKGKVPACVETCPTYCRTFGDLEDPESPVAKALKAAERVDVLRPEQGTRPKLFYLNAPSKKGLTRESEVHHG

Entity 3 Entity 3 polymer

Description description	HYPOTHETICAL MEMBRANE SPANNING PROTEIN
Molecular weight formula_weight	27623.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

MAEFYGLPNAQEFWHWTNALHFVLVGLAGGVALLAALLHLKGDAEARRYTLYALMLIALDLFILWAESPARFRFTHIWLFLSFHPTSPIWWGAWGLGLGFLTGGLLYLGKGSQRALAWALLVFSLVALSYPGLALAVNLNRPLWNGLMAGLFPLTALVLALGLAALLKSPWALFPLRVLAGASLLLALLYPLTLPPEARGHLLEEAGFWYGLFLLLGLGTFWQERLAPWAGLLAAAGLRALLVLAGQWQGLGL

Entity 4 Entity 4 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
Molecular weight formula_weight	740.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	MOLYBDENUM ATOM
Molecular weight formula_weight	95.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	PENTACHLOROPHENOL
Molecular weight formula_weight	266.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1285

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	2vpyA01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	90 — ADC-like domains

Domain ID domain_id	2vpyA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	2vpyA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	2vpyA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2070 — Formate dehydrogenase/DMSO reductase,
Homologous superfamily homologous superfamily	10 — Formate dehydrogenase/DMSO reductase,

Domain ID domain_id	2vpyA05
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2vpyB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2vpyB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2vpyC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1630 — Formate dehydrogenase/DMSO reductase fold
Homologous superfamily homologous superfamily	10 — Formate dehydrogenase/DMSO reductase domain

Domain ID domain_id	2vpyE01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	90 — ADC-like domains

Domain ID domain_id	2vpyE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	2vpyE03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

Domain ID domain_id	2vpyE04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2070 — Formate dehydrogenase/DMSO reductase,
Homologous superfamily homologous superfamily	10 — Formate dehydrogenase/DMSO reductase,

Domain ID domain_id	2vpyE05
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2vpyF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2vpyF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2vpyG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1630 — Formate dehydrogenase/DMSO reductase fold
Homologous superfamily homologous superfamily	10 — Formate dehydrogenase/DMSO reductase domain

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Unit-cell length a length_a	117.124 Å
Unit-cell length b length_b	165.194 Å
Unit-cell length c length_c	243.153 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	39.580 Å
R factor r_factor	0.2830
R_work r_work	0.2830
R_free r_free	0.2890

Polysulfide reductase with bound quinone inhibitor, pentachlorophenol (PCP)

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

THIOSULFATE REDUCTASE

State in the Current Structure

Other States of the Same Protein in the Database

NRFC PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

HYPOTHETICAL MEMBRANE SPANNING 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

2vpy__assembly_1__model_1

2vpy__assembly_1__model_1 | I(q)

2vpy__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Polysulfide reductase with bound quinone inhibitor, pentachlorophenol (PCP)

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

THIOSULFATE REDUCTASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NRFC 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

HYPOTHETICAL MEMBRANE SPANNING 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

2vpy__assembly_1__model_1

2vpy__assembly_1__model_1 | I(q)

2vpy__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)