SAXSdb — 1ml4

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

Aspartate Transcarbamoylase

Pyrococcus abyssi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	N-(PHOSPHONACETYL)-L-ASPARTIC ACID × 3 water × 3	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N-(PHOSPHONACETYL)-L-ASPARTIC ACID × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	N-(PHOSPHONACETYL)-L-ASPARTIC ACID × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRB_PYRAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–308； UniProt 1–308

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	1ml4
Deposition date deposition_date	2002-08-30
Structure title title	The PALA-liganded Aspartate transcarbamoylase catalytic subunit from Pyrococcus abyssi
Keywords keywords	BETA PLEATED SHEET, PROTEIN INHIBITOR COMPLEX, TRANSFERASE; TRANSFERASE
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.

1ml4__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ml4__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ml4__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.32 Å
Rg (electron density)	19.29 Å
Total Rg	20.26 Å
Atom count	2466
Residues	307
Excluded volume	44311 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ml4__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ml4__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1ml4__assembly_3__model_1`	trimeric （3）	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	Aspartate Transcarbamoylase
Molecular weight formula_weight	34954.4 kDa
EC 编号 ec_number	2.1.3.2
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	2543

MDWKGRDVISIRDFSKEDIETVLATAERLERELKEKGQLEYAKGKILATLFFEPSTRTRLSFESAMHRLGGAVIGFAEASTSSVKKGESLRDTIKTVEQYCDVIVIRHPKEGAARLAAEVAEVPVINAGDGSNQHPTQTLLDLYTIKKEFGRIDGLKIGLLGDLKYGRTVHSLAEALTFYDVELYLISPELLRMPRHIVEELREKGMKVVETTTLEDVIGKLDVLYVTRIQKERFPDEQEYLKVKGSYQVNLKVLEKAKDELRIMHPLPRVDEIHPEVDNTKHAIYFRQVFNGVPVRMALLALVLGVI

Source Source

Source organism organism	Pyrococcus abyssi
NCBI taxonomy ID ncbi_taxonomy_id	29292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N-(PHOSPHONACETYL)-L-ASPARTIC ACID
Molecular weight formula_weight	255.1 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	77

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ml4a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	d1ml4a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.78 — ATC-like
Superfamily Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

CATH v4.4 (2 domains)

Domain ID domain_id	1ml4A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

Domain ID domain_id	1ml4A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

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Unit-cell length a length_a	81.095 Å
Unit-cell length b length_b	81.095 Å
Unit-cell length c length_c	141.959 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1760
R_work r_work	0.1720
R_free r_free	0.2120

The PALA-liganded Aspartate transcarbamoylase catalytic subunit from Pyrococcus abyssi

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

Aspartate Transcarbamoylase

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

1ml4__assembly_2__model_1

1ml4__assembly_2__model_1 | I(q)

1ml4__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The PALA-liganded Aspartate transcarbamoylase catalytic subunit from Pyrococcus abyssi

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

Aspartate Transcarbamoylase

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

1ml4__assembly_2__model_1

1ml4__assembly_2__model_1 | I(q)

1ml4__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)