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4wkg

The crystal structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic coop-erativity

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

Bifunctional polymyxin resistance protein ArnA

OrganismNot specified

UniProt P77398

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 6 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 ACETATE ION × 2 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1u9j 1yrw 1z73 1z74 1z75 1z7b 2bln 2bln

8 assemblies

Homodimer
1u9j 2bll

2 assemblies

Homotetramer

None

Other homooligomers
1u9j 1z73 1z75 1z7e 21ak 4wkg 9v5h 9wi0

8 assemblies

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name ARNA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–660； UniProt 1–660 Author chain B； PDBConstruct 1–660； UniProt 1–660 Author chain C； PDBConstruct 1–660； UniProt 1–660 Author chain D； PDBConstruct 1–660； UniProt 1–660 Author chain E； PDBConstruct 1–660； UniProt 1–660 Author chain F； PDBConstruct 1–660； UniProt 1–660

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_id4wkg
Deposition date deposition_date2014-10-02
Structure title titleThe crystal structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic coop-erativity
Keywords keywordsArnA, multi-drug resistance, MDR, polymyxin, dehydrogenase, transformylase, cooperativity, allosteric regulation, transferase; TRANSFERASE
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.

4wkg__assembly_1__model_1

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

Download this curve (.dat)

4wkg__assembly_1__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.

4wkg__assembly_1__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）53.21 Å
Rg (electron density)52.71 Å
Total Rg53.03 Å
Atom count59955
Residues3837
Excluded volume536980 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4wkg__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 (4)

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd4wkga1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.65 — Formyltransferase
Superfamily Superfamily superfamilyc.65.1 — Formyltransferase
Family Family familyc.65.1.1 — Formyltransferase
Domain ID domain_idd4wkga2
Class classb — All beta proteins
Fold Fold foldb.46 — FMT C-terminal domain-like
Superfamily Superfamily superfamilyb.46.1 — FMT C-terminal domain-like
Family Family familyb.46.1.1 — Post formyltransferase domain
Domain ID domain_idd4wkga3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd4wkgb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.65 — Formyltransferase
Superfamily Superfamily superfamilyc.65.1 — Formyltransferase
Family Family familyc.65.1.1 — Formyltransferase
Domain ID domain_idd4wkgb2
Class classb — All beta proteins
Fold Fold foldb.46 — FMT C-terminal domain-like
Superfamily Superfamily superfamilyb.46.1 — FMT C-terminal domain-like
Family Family familyb.46.1.1 — Post formyltransferase domain
Domain ID domain_idd4wkgb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd4wkgc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.65 — Formyltransferase
Superfamily Superfamily superfamilyc.65.1 — Formyltransferase
Family Family familyc.65.1.1 — Formyltransferase
Domain ID domain_idd4wkgc2
Class classb — All beta proteins
Fold Fold foldb.46 — FMT C-terminal domain-like
Superfamily Superfamily superfamilyb.46.1 — FMT C-terminal domain-like
Family Family familyb.46.1.1 — Post formyltransferase domain
Domain ID domain_idd4wkgc3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd4wkgd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.65 — Formyltransferase
Superfamily Superfamily superfamilyc.65.1 — Formyltransferase
Family Family familyc.65.1.1 — Formyltransferase
Domain ID domain_idd4wkgd2
Class classb — All beta proteins
Fold Fold foldb.46 — FMT C-terminal domain-like
Superfamily Superfamily superfamilyb.46.1 — FMT C-terminal domain-like
Family Family familyb.46.1.1 — Post formyltransferase domain
Domain ID domain_idd4wkge1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.65 — Formyltransferase
Superfamily Superfamily superfamilyc.65.1 — Formyltransferase
Family Family familyc.65.1.1 — Formyltransferase
Domain ID domain_idd4wkge2
Class classb — All beta proteins
Fold Fold foldb.46 — FMT C-terminal domain-like
Superfamily Superfamily superfamilyb.46.1 — FMT C-terminal domain-like
Family Family familyb.46.1.1 — Post formyltransferase domain
Domain ID domain_idd4wkgf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.65 — Formyltransferase
Superfamily Superfamily superfamilyc.65.1 — Formyltransferase
Family Family familyc.65.1.1 — Formyltransferase
Domain ID domain_idd4wkgf2
Class classb — All beta proteins
Fold Fold foldb.46 — FMT C-terminal domain-like
Superfamily Superfamily superfamilyb.46.1 — FMT C-terminal domain-like
Family Family familyb.46.1.1 — Post formyltransferase domain
Domain ID domain_idd4wkgf3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (12 domains)

Domain ID domain_id4wkgA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12230 —
Domain ID domain_id4wkgA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id4wkgB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12230 —
Domain ID domain_id4wkgB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id4wkgC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12230 —
Domain ID domain_id4wkgC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id4wkgD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12230 —
Domain ID domain_id4wkgD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id4wkgE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12230 —
Domain ID domain_id4wkgE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id4wkgF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12230 —
Domain ID domain_id4wkgF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
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7. Citations (1)