SAXSdb — 9b8m

▼

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

Ornithine decarboxylase

Homo sapiens

UniProt P11926

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–422 Chain B； UniProt 1–422	Not recorded	A1AQO O-{[(3R)-pyrrolidin-3-yl]methyl}hydroxylamine × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；Not available	Resolution 2.90 Å R-free 0.223

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9B8M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D7K CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION Deposited 1999-10-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 7–427（421 aa） Chain B 7–427（421 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；20% PEG 3350, 0.2M NaCl, 5mM DTT, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, temperature 16K	Resolution 2.10 Å R-free 0.288
2ON3 A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 3-aminooxy-1-aminopropane Deposited 2007-01-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–461（461 aa） Chain B 1–461（461 aa）	Not recorded	XAP 3-AMINOOXY-1-AMINOPROPANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；288.15 K；25% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, 2 mM APA, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K	Resolution 3.00 Å R-free 0.293
2OO0 A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 3-aminooxy-1-aminopropane Deposited 2007-01-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–461（461 aa） Chain B 1–461（461 aa）	Not recorded	ACT ACETATE ION × 3 PLP PYRIDOXAL-5'-PHOSPHATE × 2 XAP 3-AMINOOXY-1-AMINOPROPANE × 2 N2P PENTANE-1,5-DIAMINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；288.15 K；25% PEG3350, 0.2 M ammonium acetate, O.1M MES, 2mM XAP, 0.3 % cadaverine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K	Resolution 1.90 Å R-free 0.213
4ZGY STRUCTURE of HUMAN ORNITHINE DECARBOXYLASE IN COMPLEX WITH A C-TERMINAL FRAGMENT OF ANTIZYME Deposited 2015-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–421（420 aa） Fragment：UNP RESIDUES 2-421	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；100MM MAGNESIUM ACETATE, 50MM MES PH 5.6, 20% 2-METHYL-2, 4-PENTANEDIOL(MPD), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K	Resolution 2.63 Å R-free 0.256
5BWA Crystal structure of ODC-PLP-AZ1 ternary complex Deposited 2015-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–461（461 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；288 K；0.2 M di-Ammonium tartrate, 20% PEG 3350	Resolution 3.20 Å R-free 0.289
7S3F Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in complex with its inhibitor 1-amino-oxy-3-aminopropane Deposited 2021-09-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–424（424 aa） Chain B 1–424（424 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 XAP 3-AMINOOXY-1-AMINOPROPANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；2% tacsimate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, and 16% w/v polyethylene glycol 3350	Resolution 2.49 Å R-free 0.208
7S3G Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in complex with citrate at the catalytic center Deposited 2021-09-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–424（424 aa） Chain B 1–424（424 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM tri-sodium citrate pH 5.0 and 30% polyethylene glycol monomethyl ether 550	Resolution 1.66 Å R-free 0.198
7U6P Structure of an intellectual disability-associated ornithine decarboxylase variant G84R Deposited 2022-03-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–424（424 aa） Chain B 1–424（424 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M sodium acetate trihydrate pH 7.0, 20% w/v polyethylene glycol 3350	Resolution 2.35 Å R-free 0.225
7U6U Structure of an intellectual disability-associated ornithine decarboxylase variant G84R in complex with PLP Deposited 2022-03-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–424（424 aa） Chain B 1–424（424 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M sodium acetate trihydrate pH 7.0, 20% w/v polyethylene glycol 3350	Resolution 1.85 Å R-free 0.204
9B8N Crystal structure of ornithine decarboxylase in complex with a novel inhibitor (10-S) Deposited 2024-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–424（424 aa） Chain B 1–424（424 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 A1AQP O-{[(3S)-pyrrolidin-3-yl]methyl}hydroxylamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；not available	Resolution 2.00 Å R-free 0.208

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DCOR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–422； UniProt 1–422 Author chain B； PDBConstruct 1–422； UniProt 1–422

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	9b8m
Deposition date deposition_date	2024-03-31
Structure title title	Crystal structure of ornithine decarboxylase in complex with a novel inhibitor
Keywords keywords	analogs, drug inhibitors, DFMO, CARBOHYDRATE; CARBOHYDRATE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.31 Å
Radius of gyration Rg (electron density) rg_electron	28.61 Å
Forward intensity I(0) i0	249040000.00
Molecular weight molecular_weight	84560.0 kDa
Excluded volume excluded_volume	82076 Å³
Envelope volume envelope_volume	139860 Å³
Hydration-shell volume shell_volume	39678 Å³
Envelope diameter envelope_diameter	99.2 Å
Shell Rg shell_rg	36.86 Å
Envelope Rg envelope_rg	28.55 Å
Shape Rg shape_rg	28.61 Å
Total Rg total_rg	29.18 Å
Total atoms total_atoms	6392
Residues n_residues	810
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	91.6 Å
Rg (real space) rg_real	29.22 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	2.4900e+08
I(0) uncertainty (real space) i0_real_error	3.4390e+06
Rg (reciprocal space) rg_reciprocal	29.26 Å
I(0) (reciprocal space) i0_reciprocal	249000000.0000
Solution quality estimate total_estimate	0.9040
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.9 Å
Skewness Skewness skewness	0.243
Kurtosis Kurtosis kurtosis	-0.491
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	57050000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.934

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ornithine decarboxylase
Molecular weight formula_weight	47029.4 kDa
EC 编号 ec_number	4.1.1.17
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	6408

MNNFGNEEFDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFEEITGVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQTGSDDEDESSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPKPDEKYYSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQLMQQFQN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	O-{[(3R)-pyrrolidin-3-yl]methyl}hydroxylamine
Molecular weight formula_weight	116.2 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

▶

8. Citations (1)

▶

Unit-cell length a length_a	74.650 Å
Unit-cell length b length_b	86.430 Å
Unit-cell length c length_c	153.220 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	31.780 Å
R factor r_factor	0.1951
R_work r_work	0.1937
R_free r_free	0.2229

fit	/app/data/saxs_computation/b8/9b8m/9b8m.fit
pddf	/app/data/pr_computation/b8/9b8m/9b8m.pr.out
profile	/app/data/saxs_computation/b8/9b8m/9b8m.dat

Crystal structure of ornithine decarboxylase in complex with a novel inhibitor

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction