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1y4z

The crystal structure of Nitrate Reductase A, NarGHI, in complex with the Q-site inhibitor pentachlorophenol

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Respiratory nitrate reductase 1 alpha chain

Escherichia coli

UniProt P09152

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Respiratory nitrate reductase 1 beta chain × 1 （P11349） Respiratory nitrate reductase 1 gamma chain × 1 （P11350） PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER × 2 MOLYBDENUM(VI) ION × 1 IRON/SULFUR CLUSTER × 3 (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE × 1 FE3-S4 CLUSTER × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 PENTACHLOROPHENOL × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Respiratory nitrate reductase 1 beta chain × 2 （P11349） Respiratory nitrate reductase 1 gamma chain × 2 （P11350） PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER × 4 MOLYBDENUM(VI) ION × 2 IRON/SULFUR CLUSTER × 6 (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE × 2 FE3-S4 CLUSTER × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 PENTACHLOROPHENOL × 2 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1q16 1q16 1q16 1q16 1r27 1r27 1r27 1r27 1r27 1siw 1siw 1siw

37 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NARG_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1246； UniProt 1–1246

Respiratory nitrate reductase 1 beta chain

Escherichia coli

UniProt P11349

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Respiratory nitrate reductase 1 alpha chain × 1 （P09152） Respiratory nitrate reductase 1 gamma chain × 1 （P11350） PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER × 2 MOLYBDENUM(VI) ION × 1 IRON/SULFUR CLUSTER × 3 (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE × 1 FE3-S4 CLUSTER × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 PENTACHLOROPHENOL × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Respiratory nitrate reductase 1 alpha chain × 2 （P09152） Respiratory nitrate reductase 1 gamma chain × 2 （P11350） PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER × 4 MOLYBDENUM(VI) ION × 2 IRON/SULFUR CLUSTER × 6 (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE × 2 FE3-S4 CLUSTER × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 PENTACHLOROPHENOL × 2 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1q16 1q16 1q16 1q16 1r27 1r27 1r27 1r27 1r27 1siw 1siw 1siw

35 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NARH_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–512； UniProt 1–512

Respiratory nitrate reductase 1 gamma chain

Escherichia coli

UniProt P11350

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Respiratory nitrate reductase 1 alpha chain × 1 （P09152） Respiratory nitrate reductase 1 beta chain × 1 （P11349） PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER × 2 MOLYBDENUM(VI) ION × 1 IRON/SULFUR CLUSTER × 3 (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE × 1 FE3-S4 CLUSTER × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 PENTACHLOROPHENOL × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Respiratory nitrate reductase 1 alpha chain × 2 （P09152） Respiratory nitrate reductase 1 beta chain × 2 （P11349） PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER × 4 MOLYBDENUM(VI) ION × 2 IRON/SULFUR CLUSTER × 6 (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE × 2 FE3-S4 CLUSTER × 4 PROTOPORPHYRIN IX CONTAINING FE × 4 PENTACHLOROPHENOL × 2 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1q16 1q16 1q16 1q16 1siw 1siw 1siw 1siw 1y4z 1y4z 1y5i 1y5i

30 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NARI_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–225； UniProt 1–225

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_id1y4z
Deposition date deposition_date2004-12-01
Structure title titleThe crystal structure of Nitrate Reductase A, NarGHI, in complex with the Q-site inhibitor pentachlorophenol
Keywords keywordsnitrate reduction, electron transfer, membrane protein, Q-site, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-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.

1y4z__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1y4z__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1y4z__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）46.95 Å
Rg (electron density)46.78 Å
Total Rg46.92 Å
Atom count31798
Residues3938
Excluded volume564170 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1y4z__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1y4z__assembly_2__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 (11)

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1y4za1
Class classb — All beta proteins
Fold Fold foldb.52 — Double psi beta-barrel
Superfamily Superfamily superfamilyb.52.2 — ADC-like
Family Family familyb.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain
Domain ID domain_idd1y4za2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamilyc.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family familyc.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Domain ID domain_idd1y4zb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.1 — 4Fe-4S ferredoxins
Family Family familyd.58.1.5 — Ferredoxin domains from multidomain proteins
Domain ID domain_idd1y4zc_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.21 — Heme-binding four-helical bundle
Superfamily Superfamily superfamilyf.21.3 — Respiratory nitrate reductase 1 gamma chain
Family Family familyf.21.3.1 — Respiratory nitrate reductase 1 gamma chain

CATH v4.4 (5 domains)

Domain ID domain_id1y4zA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12770 — Nitrate reductase alpha subunit
Domain ID domain_id1y4zA04
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1y4zB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1y4zB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3650 — nitrate reductase domain fold
Homologous superfamily homologous superfamily10 — nitrate reductase domain like
Domain ID domain_id1y4zC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology950 — Fumarate Reductase Cytochrome B subunit
Homologous superfamily homologous superfamily20 — Transmembrane di-heme cytochromes, Chain C
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7. Citations (1)