1f3t

CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.

Method: X-RAY DIFFRACTION

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

ORNITHINE DECARBOXYLASE

Trypanosoma brucei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PYRIDOXAL-5'-PHOSPHATE × 2 1,4-DIAMINOBUTANE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PYRIDOXAL-5'-PHOSPHATE × 2 1,4-DIAMINOBUTANE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCOR_TRYBB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–425； UniProt 1–423 Author chain B； PDBConstruct 3–425； UniProt 1–423 Author chain C； PDBConstruct 3–425； UniProt 1–423 Author chain D； PDBConstruct 3–425； UniProt 1–423

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	1f3t
Deposition date deposition_date	2000-06-06
Structure title title	CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.
Keywords keywords	beta-alpha-barrel, modified Greek key beta-sheet, LYASE; LYASE
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.

1f3t__assembly_1__model_1

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

Download this curve (.dat)

1f3t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1f3t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.13 Å
Rg (electron density)	28.46 Å
Total Rg	29.27 Å
Atom count	5994
Residues	759
Excluded volume	107180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1f3t__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1f3t__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	ORNITHINE DECARBOXYLASE
Molecular weight formula_weight	47062.5 kDa
EC 编号 ec_number	4.1.1.17
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12201

GAMDIVVNDDLSCRFLEGFNTRDALCKKISMNTCDEGDPFFVADLGDIVRKHETWKKCLPRVTPFYAVKCNDDWRVLGTLAALGTGFDCASNTEIQRVRGIGVPPEKIIYANPCKQISHIRYARDSGVDVMTFDCVDELEKVAKTHPKAKMVLRISTDDSLARCRLSVKFGAKVEDCRFILEQAKKLNIDVTGVSFHVGSGSTDASTFAQAISDSRFVFDMGTELGFNMHILDIGGGFPGTRDAPLKFEEIAGVINNALEKHFPPDLKLTIVAEPGRYYVASAFTLAVNVIAKKVTPGVQTDVGAHAESNAQSFMYYVNDGVYGSFNCILYDHAVVRPLPQREPIPNEKLYPSSVWGPTCDGLDQIVERYYLPEMQVGEWLLFEDMGAYTVVGTSSFNGFQSPTIYYVVSGLPDHVVRELKSQKS

Source Source

Source organism organism	Trypanosoma brucei
NCBI taxonomy ID ncbi_taxonomy_id	5691
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1,4-DIAMINOBUTANE
Molecular weight formula_weight	88.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	380

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1f3ta1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
Family Family family	b.49.2.3 — Eukaryotic ODC-like

Domain ID domain_id	d1f3ta2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.6 — PLP-binding barrel
Family Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

Domain ID domain_id	d1f3tb1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
Family Family family	b.49.2.3 — Eukaryotic ODC-like

Domain ID domain_id	d1f3tb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.6 — PLP-binding barrel
Family Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

Domain ID domain_id	d1f3tc1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
Family Family family	b.49.2.3 — Eukaryotic ODC-like

Domain ID domain_id	d1f3tc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.6 — PLP-binding barrel
Family Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

Domain ID domain_id	d1f3td1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
Family Family family	b.49.2.3 — Eukaryotic ODC-like

Domain ID domain_id	d1f3td2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.6 — PLP-binding barrel
Family Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1f3tA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

Domain ID domain_id	1f3tA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	10 — Alanine racemase

Domain ID domain_id	1f3tB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

Domain ID domain_id	1f3tB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	10 — Alanine racemase

Domain ID domain_id	1f3tC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

Domain ID domain_id	1f3tC02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	10 — Alanine racemase

Domain ID domain_id	1f3tD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

Domain ID domain_id	1f3tD02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	10 — Alanine racemase

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Unit-cell length a length_a	67.294 Å
Unit-cell length b length_b	151.599 Å
Unit-cell length c length_c	86.414 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2370
R_free r_free	0.2800

CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.

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

ORNITHINE DECARBOXYLASE

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

1f3t__assembly_1__model_1

1f3t__assembly_1__model_1 | I(q)

1f3t__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.

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

ORNITHINE DECARBOXYLASE

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

1f3t__assembly_1__model_1

1f3t__assembly_1__model_1 | I(q)

1f3t__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)