SAXSdb — 6a89

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptidoglycan recognition protein 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 1 2,6-DIAMINOPIMELIC ACID × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 L(+)-TARTARIC ACID × 1 alpha-D-ribofuranose × 1 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	2,6-DIAMINOPIMELIC ACID × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 L(+)-TARTARIC ACID × 1 alpha-D-ribofuranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PGRP1_CAMDR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 27–193 Author chain B； PDBConstruct 1–167； UniProt 27–193 Author chain C； PDBConstruct 1–167； UniProt 27–193 Author chain D； PDBConstruct 1–167； UniProt 27–193

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_id	6a89
Deposition date deposition_date	2018-07-06
Structure title title	Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S) with Tartaric acid, Ribose and 2,6-DIAMINOPIMELIC ACID at 2.11 A resolution
Keywords keywords	IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-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.

6a89__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6a89__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6a89__assembly_5__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	15.87 Å
Rg (electron density)	14.53 Å
Total Rg	15.71 Å
Atom count	1305
Residues	167
Excluded volume	22851 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6a89__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6a89__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6a89__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6a89__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6a89__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6a89__assembly_6__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 (7)

Entity 1 Entity 1 polymer

Description description	Peptidoglycan recognition protein 1
Molecular weight formula_weight	18573.0 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5559

ACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2,6-DIAMINOPIMELIC ACID
Molecular weight formula_weight	190.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	alpha-D-ribofuranose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	293

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6a89a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.118 — N-acetylmuramoyl-L-alanine amidase-like
Superfamily Superfamily superfamily	d.118.1 — N-acetylmuramoyl-L-alanine amidase-like
Family Family family	d.118.1.1 — N-acetylmuramoyl-L-alanine amidase-like

Domain ID domain_id	d6a89b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.118 — N-acetylmuramoyl-L-alanine amidase-like
Superfamily Superfamily superfamily	d.118.1 — N-acetylmuramoyl-L-alanine amidase-like
Family Family family	d.118.1.1 — N-acetylmuramoyl-L-alanine amidase-like

Domain ID domain_id	d6a89c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.118 — N-acetylmuramoyl-L-alanine amidase-like
Superfamily Superfamily superfamily	d.118.1 — N-acetylmuramoyl-L-alanine amidase-like
Family Family family	d.118.1.1 — N-acetylmuramoyl-L-alanine amidase-like

Domain ID domain_id	d6a89d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.118 — N-acetylmuramoyl-L-alanine amidase-like
Superfamily Superfamily superfamily	d.118.1 — N-acetylmuramoyl-L-alanine amidase-like
Family Family family	d.118.1.1 — N-acetylmuramoyl-L-alanine amidase-like

CATH v4.4 (4 domains)

Domain ID domain_id	6a89A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	80 — Lysozyme-like
Homologous superfamily homologous superfamily	10 — Peptidoglycan recognition protein-like

Domain ID domain_id	6a89B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	80 — Lysozyme-like
Homologous superfamily homologous superfamily	10 — Peptidoglycan recognition protein-like

Domain ID domain_id	6a89C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	80 — Lysozyme-like
Homologous superfamily homologous superfamily	10 — Peptidoglycan recognition protein-like

Domain ID domain_id	6a89D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	80 — Lysozyme-like
Homologous superfamily homologous superfamily	10 — Peptidoglycan recognition protein-like

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Unit-cell length a length_a	89.500 Å
Unit-cell length b length_b	101.370 Å
Unit-cell length c length_c	163.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.110 Å
Low-resolution limit resolution_low	86.090 Å
R factor r_factor	0.1936
R_work r_work	0.1907
R_free r_free	0.2488

Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S) with Tartaric acid, Ribose and 2,6-DIAMINOPIMELIC ACID at 2.11 A resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptidoglycan recognition protein 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6a89__assembly_5__model_1

6a89__assembly_5__model_1 | I(q)

6a89__assembly_5__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S) with Tartaric acid, Ribose and 2,6-DIAMINOPIMELIC ACID at 2.11 A resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptidoglycan recognition protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6a89__assembly_5__model_1

6a89__assembly_5__model_1 | I(q)

6a89__assembly_5__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)