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2rkm

STRUCTURE OF OPPA COMPLEXED WITH LYS-LYS

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

OLIGO-PEPTIDE BINDING PROTEIN

OrganismNot specified

UniProt P06202

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 LYSINE × 2 URANYL (VI) ION × 8 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1rkm 2rkm

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1b05 1b1h 1b2h 1b32 1b3f 1b3g 1b3h 1b3l 1b3l 1b40 1b46 1b4z

29 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name OPPA_SALTY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–517； UniProt 26–542

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_id2rkm
Deposition date deposition_date1997-03-25
Structure title titleSTRUCTURE OF OPPA COMPLEXED WITH LYS-LYS
Keywords keywordsPEPTIDE TRANSPORT, COMPLEX (BINDING PROTEIN-DIPEPTIDE), Peptide BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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.

2rkm__assembly_1__model_1

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

Download this curve (.dat)

2rkm__assembly_1__model_1 | I(q)

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

2rkm__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）24.76 Å
Rg (electron density)23.46 Å
Total Rg24.84 Å
Atom count4207
Residues517
Excluded volume74970 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2rkm__assembly_1__model_1 monomeric （1） 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) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2rkma_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like

CATH v4.4 (3 domains)

Domain ID domain_id2rkmA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id2rkmA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily10 — Dipeptide-binding Protein; Domain 1
Domain ID domain_id2rkmA03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily10 — Dipeptide-binding Protein; Domain 3
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7. Citations (5)