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1pyy

Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution

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

Penicillin-binding protein 2X

Streptococcus pneumoniae

UniProt P59676

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Monomer Protein 1 其他Polymer 1 6-O-octanoyl-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 SULFATE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5oau 5oiz 5oj0 5oj1

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
2z2l 2z2l 2z2m 2z2m 2zc3 2zc3 2zc3 2zc4 2zc4 2zc4

10 assemblies

Heteromeric or nucleic-acid complex
1pyy

1 assemblies

View Construct and Data Evidence
UniProt name PBPX_STRR6
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–702； UniProt 49–750

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_id1pyy
Deposition date deposition_date2003-07-09
Structure title titleDouble mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution
Keywords keywordsPENICILLIN-BINDING PROTEIN, ANTIBIOTIC RESISTANCE, PEPTIDOGLYCAN SYNTHESIS, CELL WALL, TRANSMEMBRANE, TRANSPEPTIDASE; TRANSPEPTIDASE
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.

1pyy__assembly_1__model_1

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

Download this curve (.dat)

1pyy__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.

1pyy__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）27.40 Å
Rg (electron density)26.83 Å
Total Rg27.48 Å
Atom count4687
Residues607
Excluded volume83100 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1pyy__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 (5)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1pyya1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamilyd.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family familyd.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Domain ID domain_idd1pyya2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamilyd.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family familyd.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Domain ID domain_idd1pyya3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.175 — Penicillin binding protein dimerisation domain
Superfamily Superfamily superfamilyd.175.1 — Penicillin binding protein dimerisation domain
Family Family familyd.175.1.1 — Penicillin binding protein dimerisation domain
Domain ID domain_idd1pyya4
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (2 domains)

Domain ID domain_id1pyyA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1310 — Penicillin-binding protein 2a (Domain 2)
Homologous superfamily homologous superfamily10 — Penicillin-binding protein 2a (Domain 2)
Domain ID domain_id1pyyA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
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7. Citations (4)