SAXSdb — 2ekl

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

D-3-phosphoglycerate dehydrogenase

Sulfolobus tokodaii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q972A9_SULTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–313； UniProt 1–313

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	2ekl
Deposition date deposition_date	2007-03-23
Structure title title	Structure of ST1218 protein from Sulfolobus tokodaii
Keywords keywords	;phosphoglycerate dehydrogenase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

2ekl__assembly_1__model_1

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

Download this curve (.dat)

2ekl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ekl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.39 Å
Rg (electron density)	29.27 Å
Total Rg	29.82 Å
Atom count	4934
Residues	624
Excluded volume	89695 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ekl__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	D-3-phosphoglycerate dehydrogenase
Molecular weight formula_weight	34706.8 kDa
EC 编号 ec_number	1.1.1.95
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	2862

MAIYTVKALITDPIDEILIKTLREKGIQVDYMPEISKEELLNIIGNYDIIVVRSRTKVTKDVIEKGKKLKIIARAGIGLDNIDTEEAEKRNIKVVYAPGASTDSAVELTIGLMIAAARKMYTSMALAKSGIFKKIEGLELAGKTIGIVGFGRIGTKVGIIANAMGMKVLAYDILDIREKAEKINAKAVSLEELLKNSDVISLHVTVSKDAKPIIDYPQFELMKDNVIIVNTSRAVAVNGKALLDYIKKGKVYAYATDVFWNEPPKEEWELELLKHERVIVTTHIGAQTKEAQKRVAEMTTQNLLNAMKELGMI

Source Source

Source organism organism	Sulfolobus tokodaii
NCBI taxonomy ID ncbi_taxonomy_id	111955
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 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	395

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2eklA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2eklA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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Unit-cell length a length_a	105.065 Å
Unit-cell length b length_b	59.798 Å
Unit-cell length c length_c	60.728 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.770 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.2200

Structure of ST1218 protein from Sulfolobus tokodaii

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

D-3-phosphoglycerate dehydrogenase

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

2ekl__assembly_1__model_1

2ekl__assembly_1__model_1 | I(q)

2ekl__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

CATH v4.4 (2 domains)

7. Citations (1)

Structure of ST1218 protein from Sulfolobus tokodaii

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

D-3-phosphoglycerate dehydrogenase

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

2ekl__assembly_1__model_1

2ekl__assembly_1__model_1 | I(q)

2ekl__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

CATH v4.4 (2 domains)

7. Citations (1)