SAXSdb — 3d3h

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

Penicillin-insensitive transglycosylase

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;(2R)-3-{[(S)-{[(2R,3R,4R,5S,6S)-3-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-5-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-5-{[(2R,3R,4S,5R,6S)-6-carbamoyl-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}methyl)tetrahydro-2H-pyran-2-yl]oxy}-6-carbamoyl-4-(carbamoyloxy)-5-hydroxy-5-methyltetrahydro-2H-pyran-2-yl]oxy}(hydroxy)phosphoryl]oxy}-2-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}propanoic acid ; × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PBPA_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–200； UniProt 51–243

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	3d3h
Deposition date deposition_date	2008-05-11
Structure title title	Crystal structure of a complex of the peptidoglycan glycosyltransferase domain from Aquifex aeolicus and neryl moenomycin A
Keywords keywords	;peptidoglycan glycosyltransferase, cell wall biosynthesis, antibiotics, penicillin-binding protein, transglycosylase, moenomycin, Antibiotic resistance, Cell shape, Cell wall biogenesis/degradation, Hydrolase, Inner membrane, Membrane, Multifunctional enzyme, Peptidoglycan synthesis, Signal-anchor, Transmembrane, TRANSFERASE-ANTIBIOTIC COMPLEX ;; TRANSFERASE/ANTIBIOTIC
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.

3d3h__assembly_1__model_1

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

Download this curve (.dat)

3d3h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d3h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.71 Å
Rg (electron density)	22.75 Å
Total Rg	23.63 Å
Atom count	3018
Residues	348
Excluded volume	54179 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d3h__assembly_1__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Penicillin-insensitive transglycosylase
Molecular weight formula_weight	22912.4 kDa
EC 编号 ec_number	2.4.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1557

GPGYQDPKGRLYGTIGIQKRFYVSIDKIPEHVINAFVATEDRNFWHHFGIDPVAIVRAAIVNYRAGRIVQGGSTITQQLAKNLFLTRERTLERKIKEALLAIKIERTFDKKKIMELYLNQIYLGSGAYGVEAAAQVYFGKHVWELSLDEAALLAALPKAPAKYNPFYHPERALQRRNLVLKRMLEEGYITPEQYEEAVNK

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(2R)-3-{[(S)-{[(2R,3R,4R,5S,6S)-3-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-5-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-5-{[(2R,3R,4S,5R,6S)-6-carbamoyl-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}methyl)tetrahydro-2H-pyran-2-yl]oxy}-6-carbamoyl-4-(carbamoyloxy)-5-hydroxy-5-methyltetrahydro-2H-pyran-2-yl]oxy}(hydroxy)phosphoryl]oxy}-2-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}propanoic acid ;
Molecular weight formula_weight	1282.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3d3ha_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.2 — Lysozyme-like
Superfamily Superfamily superfamily	d.2.1 — Lysozyme-like
Family Family family	d.2.1.10 — PBP transglycosylase domain-like

CATH v4.4 (1 domains)

Domain ID domain_id	3d3hA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3810 — Penicillin binding protein transpeptidase fold
Homologous superfamily homologous superfamily	10 — Biosynthetic peptidoglycan transglycosylase-like

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Unit-cell length a length_a	54.939 Å
Unit-cell length b length_b	100.448 Å
Unit-cell length c length_c	104.022 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	8

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

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	28.590 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2600

Crystal structure of a complex of the peptidoglycan glycosyltransferase domain from Aquifex aeolicus and neryl moenomycin A

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

Penicillin-insensitive transglycosylase

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

3d3h__assembly_1__model_1

3d3h__assembly_1__model_1 | I(q)

3d3h__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of a complex of the peptidoglycan glycosyltransferase domain from Aquifex aeolicus and neryl moenomycin A

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

Penicillin-insensitive transglycosylase

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

3d3h__assembly_1__model_1

3d3h__assembly_1__model_1 | I(q)

3d3h__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)