1rxs

E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex

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

Uridine phosphorylase

Escherichia coli

UniProt P12758

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 6 POTASSIUM ION × 3 META VANADATE × 4 PHOSPHATE ION × 5 2'-DEOXYURIDINE × 5 water × 6 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 6 POTASSIUM ION × 3 META VANADATE × 4 PHOSPHATE ION × 5 2'-DEOXYURIDINE × 5 water × 6 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 6 POTASSIUM ION × 3 META VANADATE × 4 PHOSPHATE ION × 6 2'-DEOXYURIDINE × 6 water × 6 Consistent with protein count
4 Protein homooligomer Homooligomer Protein 6 POTASSIUM ION × 3 META VANADATE × 4 PHOSPHATE ION × 5 2'-DEOXYURIDINE × 5 water × 6 Consistent with protein count
5 Protein homooligomer Homooligomer Protein 6 POTASSIUM ION × 3 META VANADATE × 4 PHOSPHATE ION × 4 2'-DEOXYURIDINE × 4 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name UDP_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–253; UniProt 0–252 Author chain B; PDBConstruct 1–253; UniProt 0–252 Author chain C; PDBConstruct 1–253; UniProt 0–252 Author chain D; PDBConstruct 1–253; UniProt 0–252 Author chain E; PDBConstruct 1–253; UniProt 0–252 Author chain F; PDBConstruct 1–253; UniProt 0–252 Author chain G; PDBConstruct 1–253; UniProt 0–252 Author chain H; PDBConstruct 1–253; UniProt 0–252 Author chain I; PDBConstruct 1–253; UniProt 0–252 Author chain J; PDBConstruct 1–253; UniProt 0–252 Author chain K; PDBConstruct 1–253; UniProt 0–252 Author chain L; PDBConstruct 1–253; UniProt 0–252 Author chain M; PDBConstruct 1–253; UniProt 0–252 Author chain N; PDBConstruct 1–253; UniProt 0–252 Author chain O; PDBConstruct 1–253; UniProt 0–252 Author chain P; PDBConstruct 1–253; UniProt 0–252 Author chain Q; PDBConstruct 1–253; UniProt 0–252 Author chain R; PDBConstruct 1–253; UniProt 0–252 Author chain a; PDBConstruct 1–253; UniProt 0–252 Author chain b; PDBConstruct 1–253; UniProt 0–252 Author chain c; PDBConstruct 1–253; UniProt 0–252 Author chain d; PDBConstruct 1–253; UniProt 0–252 Author chain e; PDBConstruct 1–253; UniProt 0–252 Author chain h; PDBConstruct 1–253; UniProt 0–252 Author chain i; PDBConstruct 1–253; UniProt 0–252 Author chain j; PDBConstruct 1–253; UniProt 0–252 Author chain k; PDBConstruct 1–253; UniProt 0–252 Author chain l; PDBConstruct 1–253; UniProt 0–252 Author chain m; PDBConstruct 1–253; UniProt 0–252 Author chain o; PDBConstruct 1–253; UniProt 0–252

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_id1rxs
Deposition date deposition_date2003-12-18
Structure title titleE. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex
Keywords keywords;pentosyltransferase, uridine phosphorylase, 2'-deoxyuridine, induced fit, specificity, potassium, 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.

1rxs__assembly_1__model_1

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

Download this curve (.dat)

1rxs__assembly_1__model_1 | I(q)

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

1rxs__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)33.30 Å
Rg (electron density)32.83 Å
Total Rg33.39 Å
Atom count11185
Residues1468
Excluded volume199090 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1rxs__assembly_1__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1rxs__assembly_2__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1rxs__assembly_3__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1rxs__assembly_4__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1rxs__assembly_5__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 (6)

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (18 domains)

Domain ID domain_idd1rxsa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxse_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsf_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsg_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsh_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsi_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsj_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsk_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsl_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsm_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsn_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxso_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsp_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsq_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases
Domain ID domain_idd1rxsr_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases

CATH v4.4 (30 domains)

Domain ID domain_id1rxsA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsF00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsG00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsH00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsI00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsJ00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsK00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsL00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsM00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsN00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsO00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsP00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsQ00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsR00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsa00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsb00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsc00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsd00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxse00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsh00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsi00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsj00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsk00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsl00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxsm00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
Domain ID domain_id1rxso00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
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7. Citations (1)