SAXSdb — 8a5w

▼

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

Phosphoserine aminotransferase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	(2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid × 2 PHOSPHOSERINE × 4 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 1 SULFATE ION × 2 water × 8	Review required
2	Protein homooligomer	Homooligomer	Protein 8	(2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid × 2 PHOSPHOSERINE × 4 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 1 SULFATE ION × 2 water × 8	Review required
3	Protein homooligomer	Homooligomer	Protein 8	(2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid × 2 PHOSPHOSERINE × 4 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 1 SULFATE ION × 2 water × 8	Review required
4	Protein homooligomer	Homooligomer	Protein 7	(2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid × 2 PHOSPHOSERINE × 3 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 1 SULFATE ION × 2 water × 7	Review required

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SERC_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–365； UniProt 6–370 Author chain D； PDBConstruct 1–365； UniProt 6–370 Author chain F； PDBConstruct 1–365； UniProt 6–370 Author chain B； PDBConstruct 24–393； UniProt 1–370 Author chain C； PDBConstruct 24–393； UniProt 1–370 Author chain E； PDBConstruct 24–393； UniProt 1–370 Author chain G； PDBConstruct 24–393； UniProt 1–370 Author chain H； PDBConstruct 24–393； UniProt 1–370

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8a5w
Deposition date deposition_date	2022-06-16
Structure title title	Crystal structure of the human phosphoserine aminotransferase (PSAT) in complex with O-phosphoserine
Keywords keywords	TRANSFERASE, human, PSAT; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

8a5w__assembly_2__model_1

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

Download this curve (.dat)

8a5w__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8a5w__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	52.17 Å
Rg (electron density)	51.52 Å
Total Rg	51.65 Å
Atom count	22632
Residues	2916
Excluded volume	406330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8a5w__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8a5w__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8a5w__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`8a5w__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Phosphoserine aminotransferase
Molecular weight formula_weight	39894.9 kDa
EC 编号 ec_number	2.6.1.52
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,A
Atom count atom_count	22746

QVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Phosphoserine aminotransferase
Molecular weight formula_weight	43133.4 kDa
EC 编号 ec_number	2.6.1.52
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,C,B,G,H

MGSSHHHHHHSSGLVPRGSHIGPMDAPRQVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	(2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid
Molecular weight formula_weight	414.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOSERINE
Molecular weight formula_weight	185.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	248.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8a5wA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	8a5wA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

▶

Unit-cell length a length_a	65.433 Å
Unit-cell length b length_b	205.742 Å
Unit-cell length c length_c	135.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.780 Å
Low-resolution limit resolution_low	51.440 Å
R factor r_factor	0.1844
R_work r_work	0.1821
R_free r_free	0.2276

Crystal structure of the human phosphoserine aminotransferase (PSAT) in complex with O-phosphoserine

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

Phosphoserine aminotransferase

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

8a5w__assembly_2__model_1

8a5w__assembly_2__model_1 | I(q)

8a5w__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the human phosphoserine aminotransferase (PSAT) in complex with O-phosphoserine

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

Phosphoserine aminotransferase

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

8a5w__assembly_2__model_1

8a5w__assembly_2__model_1 | I(q)

8a5w__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)