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3nw3

Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with the PGN Fragment at 2.5 A resolution

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

Peptidoglycan recognition protein 1

OrganismNot specified

UniProt Q9GK12

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 L(+)-TARTARIC ACID × 1 GLYCEROL × 1 D-GLUTAMINE × 1 ALANINE × 1 LACTIC ACID × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5dwf 5dwf 5dwf 5dwf 6a89 6a89 6a89 6a89

8 assemblies

Homodimer
3c2x 3c2x 3cxa 4orv 4orv 4oug 4oug 4q8s 4q8s 5e0b 5e0b 6a89

25 assemblies; showing the first 12

Homotetramer
2r90 2z9n 3cg9 3cor 3nno 3nw3 3o4k 3qj1 3qs0 3rt4 3t2v 3t39

22 assemblies; showing the first 12

Other homooligomers

None

Heteromeric or nucleic-acid complex
2r2k 3cxa 3cxa 3cxa 3ng4 3ogx 3qv4

7 assemblies

View Construct and Data Evidence
UniProt name PGRP1_CAMDR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–171； UniProt 23–193 Author chain B； PDBConstruct 1–171； UniProt 23–193 Author chain C； PDBConstruct 1–171； UniProt 23–193 Author chain D； PDBConstruct 1–171； UniProt 23–193

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_id3nw3
Deposition date deposition_date2010-07-09
Structure title titleCrystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with the PGN Fragment at 2.5 A resolution
Keywords keywordsImmune response, secreted, antimicrobial, PGRP, Antibiotic, Peptidoglycan Binding, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

3nw3__assembly_1__model_1

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

Download this curve (.dat)

3nw3__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.

3nw3__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）29.56 Å
Rg (electron density)28.72 Å
Total Rg29.43 Å
Atom count5398
Residues684
Excluded volume94404 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3nw3__assembly_1__model_1 tetrameric （4） 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 (8)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3nw3a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.118 — N-acetylmuramoyl-L-alanine amidase-like
Superfamily Superfamily superfamilyd.118.1 — N-acetylmuramoyl-L-alanine amidase-like
Family Family familyd.118.1.1 — N-acetylmuramoyl-L-alanine amidase-like
Domain ID domain_idd3nw3b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.118 — N-acetylmuramoyl-L-alanine amidase-like
Superfamily Superfamily superfamilyd.118.1 — N-acetylmuramoyl-L-alanine amidase-like
Family Family familyd.118.1.1 — N-acetylmuramoyl-L-alanine amidase-like
Domain ID domain_idd3nw3c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.118 — N-acetylmuramoyl-L-alanine amidase-like
Superfamily Superfamily superfamilyd.118.1 — N-acetylmuramoyl-L-alanine amidase-like
Family Family familyd.118.1.1 — N-acetylmuramoyl-L-alanine amidase-like
Domain ID domain_idd3nw3d_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.118 — N-acetylmuramoyl-L-alanine amidase-like
Superfamily Superfamily superfamilyd.118.1 — N-acetylmuramoyl-L-alanine amidase-like
Family Family familyd.118.1.1 — N-acetylmuramoyl-L-alanine amidase-like

CATH v4.4 (4 domains)

Domain ID domain_id3nw3A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology80 — Lysozyme-like
Homologous superfamily homologous superfamily10 — Peptidoglycan recognition protein-like
Domain ID domain_id3nw3B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology80 — Lysozyme-like
Homologous superfamily homologous superfamily10 — Peptidoglycan recognition protein-like
Domain ID domain_id3nw3C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology80 — Lysozyme-like
Homologous superfamily homologous superfamily10 — Peptidoglycan recognition protein-like
Domain ID domain_id3nw3D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology80 — Lysozyme-like
Homologous superfamily homologous superfamily10 — Peptidoglycan recognition protein-like
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7. Citations (1)