1njj

Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418

Method: X-RAY DIFFRACTION

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

ornithine decarboxylase

Trypanosoma brucei gambiense

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GENETICIN × 2 N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GENETICIN × 1 N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9TZZ6_TRYBG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–425； UniProt 21–445 Author chain B； PDBConstruct 1–425； UniProt 21–445 Author chain C； PDBConstruct 1–425； UniProt 21–445 Author chain D； PDBConstruct 1–425； UniProt 21–445

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	1njj
Deposition date deposition_date	2002-12-31
Structure title title	Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418
Keywords keywords	;ornithine decarboxylase, ODC, PLP, pyridoxal 5'-phosphate, D-ornithine, G418, 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.

1njj__assembly_2__model_1

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

Download this curve (.dat)

1njj__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1njj__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.04 Å
Rg (electron density)	28.38 Å
Total Rg	29.20 Å
Atom count	5629
Residues	706
Excluded volume	100770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1njj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1njj__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	47150.6 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	11424

KSMDIVVNDDLSCRFLEGFNTRDALCKKISMNTCDEGDPFFVADLGDIVRKHETWKKCLPRVTPFYAVKCNDDWRVLGTLAALGTGFDCASNTEIQRVRGIGVPPEKIIYANPCKQISHIRYARDSGVDVMTFDCVDELEKVAKTHPKAKMVLRISTDDSLARCRLSVKFGAKVEDCRFILEQAKKLNIDVTGVSFHVGSGSTDASTFAQAISDSRFVFDMGTELGFNMHILDIGGGFPGTRDAPLKFEEIAGVINNALEKHFPPDLKLTIVAEPGRYYVASAFTLAVNVIAKKVTPGVQTDVGAHAESNAQSFMYYVNDGVYGSFNCILYDHAVVRPLPQREPIPNEKLYPSSVWGPTCDGLDQIVERYYLPEMQVGEWLLFEDMGAYTVVGTSSFNGFQSPTIYYVVSGLPDHVVRELKSQKS

Source Source

Source organism organism	Trypanosoma brucei gambiense
NCBI taxonomy ID ncbi_taxonomy_id	31285
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	GENETICIN
Molecular weight formula_weight	496.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE
Molecular weight formula_weight	363.3 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	207

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1njja1
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	d1njja2
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	d1njjb1
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	d1njjb2
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	d1njjc1
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	d1njjc2
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	d1njjd1
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	d1njjd2
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	1njjA01
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	1njjA02
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	1njjB01
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	1njjB02
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	1njjC01
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	1njjC02
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	1njjD01
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	1njjD02
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	67.818 Å
Unit-cell length b length_b	88.540 Å
Unit-cell length c length_c	150.445 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.03 °
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	2.450 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	—
R_work r_work	0.2600
R_free r_free	0.2830

Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418

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

1njj__assembly_2__model_1

1njj__assembly_2__model_1 | I(q)

1njj__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 (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 determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418

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

1njj__assembly_2__model_1

1njj__assembly_2__model_1 | I(q)

1njj__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 (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)