SAXSdb — 2ehu

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

1-pyrroline-5-carboxylate dehydrogenase

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SODIUM ION × 2 ACETATE ION × 4 SERINE × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 13 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	SODIUM ION × 6 ACETATE ION × 12 SERINE × 6 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 6 (4S)-2-METHYL-2,4-PENTANEDIOL × 39 water × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	SODIUM ION × 4 ACETATE ION × 8 SERINE × 4 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 26 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SI02_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–516； UniProt 1–516 Author chain B； PDBConstruct 1–516； UniProt 1–516

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	2ehu
Deposition date deposition_date	2007-03-09
Structure title title	Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from thermus with bound NAD and Inhibitor L-serine
Keywords keywords	;Enzyme-coenzyme-inhibitor ternary complex, 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.

2ehu__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ehu__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ehu__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	40.62 Å
Rg (electron density)	39.95 Å
Total Rg	40.43 Å
Atom count	16600
Residues	2064
Excluded volume	296990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ehu__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ehu__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ehu__assembly_3__model_1`	tetrameric （4）	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	1-pyrroline-5-carboxylate dehydrogenase
Molecular weight formula_weight	57113.9 kDa
EC 编号 ec_number	1.5.1.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9304

MTVEPFRNEPIETFQTEEARRAMREALRRVREEFGRHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRIRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERF

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SERINE
Molecular weight formula_weight	105.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	988

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ehua_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.82 — ALDH-like
Superfamily Superfamily superfamily	c.82.1 — ALDH-like
Family Family family	c.82.1.1 — ALDH-like

Domain ID domain_id	d2ehub_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.82 — ALDH-like
Superfamily Superfamily superfamily	c.82.1 — ALDH-like
Family Family family	c.82.1.1 — ALDH-like

CATH v4.4 (4 domains)

Domain ID domain_id	2ehuA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

Domain ID domain_id	2ehuA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

Domain ID domain_id	2ehuB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

Domain ID domain_id	2ehuB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

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Unit-cell length a length_a	102.556 Å
Unit-cell length b length_b	102.556 Å
Unit-cell length c length_c	278.585 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	18

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	30.000 Å
R factor r_factor	0.1401
R_work r_work	0.1386
R_free r_free	0.1673

Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from thermus with bound NAD and Inhibitor L-serine

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

1-pyrroline-5-carboxylate 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

2ehu__assembly_3__model_1

2ehu__assembly_3__model_1 | I(q)

2ehu__assembly_3__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 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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from thermus with bound NAD and Inhibitor L-serine

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

1-pyrroline-5-carboxylate 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

2ehu__assembly_3__model_1

2ehu__assembly_3__model_1 | I(q)

2ehu__assembly_3__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 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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)