SAXSdb — 1d7k

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

HUMAN 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 7–427 Chain B； UniProt 7–427	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 1D7K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
9B8M Crystal structure of ornithine decarboxylase in complex with a novel inhibitor Deposited 2024-03-31	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 1–422（422 aa） Chain B 1–422（422 aa）	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
9B8N Crystal structure of ornithine decarboxylase in complex with a novel inhibitor (10-S) Deposited 2024-03-31	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 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 1–421； UniProt 7–427 Author chain B； PDBConstruct 1–421； UniProt 7–427

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	1d7k
Deposition date deposition_date	1999-10-18
Structure title title	CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION
Keywords keywords	;ALPHA-BETA BARREL, PYRIDOXAL 5'-PHOSPHATE, SHEET-DOMAIN, DECARBOXYLATION, ORNITHINE, LYASE ;; LYASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	29.77 Å
Radius of gyration Rg (electron density) rg_electron	28.92 Å
Forward intensity I(0) i0	129953000.00
Molecular weight molecular_weight	91349.0 kDa
Excluded volume excluded_volume	114830 Å³
Envelope volume envelope_volume	143630 Å³
Hydration-shell volume shell_volume	40357 Å³
Envelope diameter envelope_diameter	98.7 Å
Shell Rg shell_rg	37.18 Å
Envelope Rg envelope_rg	28.74 Å
Shape Rg shape_rg	28.92 Å
Total Rg total_rg	29.72 Å
Total atoms total_atoms	6423
Residues n_residues	817
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

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

Maximum dimension Dmax dmax	92.3 Å
Rg (real space) rg_real	29.67 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.3000e+08
I(0) uncertainty (real space) i0_real_error	2.0070e+06
Rg (reciprocal space) rg_reciprocal	29.72 Å
I(0) (reciprocal space) i0_reciprocal	130000000.0000
Solution quality estimate total_estimate	0.9042
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.8 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.495
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51040000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.922

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	HUMAN ORNITHINE DECARBOXYLASE
Molecular weight formula_weight	47161.4 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	6824

EEFDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFEEITGVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQTGSDDEDESSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPKPDERYYSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQLMQQFQNPDFPP

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	401

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d7ka1
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	d1d7ka2
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	d1d7kb1
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	d1d7kb2
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 (4 domains)

Domain ID domain_id	1d7kA01
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	1d7kA02
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	1d7kB01
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	1d7kB02
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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8. Citations (1)

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Unit-cell length a length_a	61.680 Å
Unit-cell length b length_b	107.450 Å
Unit-cell length c length_c	139.710 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	2.100 Å
Low-resolution limit resolution_low	30.500 Å
R factor r_factor	—
R_work r_work	0.2120
R_free r_free	0.2880

fit	/app/data/saxs_computation/d7/1d7k/1d7k.fit
pddf	/app/data/pr_computation/d7/1d7k/1d7k.pr.out
profile	/app/data/saxs_computation/d7/1d7k/1d7k.dat

CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION

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

HUMAN 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