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1ep9

HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CONFORMATIONAL CHANGE

Method: X-RAY DIFFRACTION Dmax: 63.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ORNITHINE TRANSCARBAMYLASE

Homo sapiens

UniProt P00480

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 34–354 Not recorded CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；20 MM TRISAC, 2MM EDTA, 20MM KCL, 4MM PALO, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 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 1EP9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C9Y HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CATALYTIC MECHANISM Deposited 1999-08-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 34–354（321 aa）
Not recorded NVA NORVALINE × 3 CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 400, AMMONIUM SULFATE, POTASSIUM CHLORIDE, EDTA, TRIS ACETATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.208
1FB5 LOW RESOLUTION STRUCTURE OF OVINE ORNITHINE TRANSCARBMOYLASE IN THE UNLIGANDED STATE Deposited 2000-07-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 35–354（320 aa）
Not recorded NVA NORVALINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 4000, 0.1 M Na acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Resolution 3.50 Å R-free 0.252
1FVO CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASE COMPLEXED WITH CARBAMOYL PHOSPHATE Deposited 2000-09-20 Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 34–354（321 aa）
Not recorded CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；291 K；Mes, PEG 8000, pH 6.5, EVAPORATION, temperature 291.0K
Resolution 2.60 Å R-free 0.236
1FVO CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASE COMPLEXED WITH CARBAMOYL PHOSPHATE Deposited 2000-09-20 Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 34–354（321 aa）
Not recorded CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；291 K；Mes, PEG 8000, pH 6.5, EVAPORATION, temperature 291.0K
Resolution 2.60 Å R-free 0.236
1OTH CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-PHOSPHONACETYL-L-ORNITHINE Deposited 1998-10-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 34–354（321 aa）
Not recorded PAO N-(PHOSPHONOACETYL)-L-ORNITHINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；20 MM TRISAC, 2MM EDTA, 20MM KCL, 4MM PALO PH=7.4, pH 7.5
Resolution 1.85 Å R-free 0.201

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OTC_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–321； UniProt 34–354

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1ep9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ep9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ep9
Deposition date deposition_date2000-03-28
Structure title titleHUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CONFORMATIONAL CHANGE
Keywords keywordsprotein-substrate complex, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.51 Å
Radius of gyration Rg (electron density) rg_electron19.39 Å
Forward intensity I(0) i021486800.00
Molecular weight molecular_weight36074.0 kDa
Excluded volume excluded_volume45531 ų
Envelope volume envelope_volume51941 ų
Hydration-shell volume shell_volume21886 ų
Envelope diameter envelope_diameter65.7 Å
Shell Rg shell_rg26.17 Å
Envelope Rg envelope_rg19.81 Å
Shape Rg shape_rg19.38 Å
Total Rg total_rg20.33 Å
Total atoms total_atoms2536
Residues n_residues320
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax63.6 Å
Rg (real space) rg_real20.40 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real2.1490e+07
I(0) uncertainty (real space) i0_real_error2.6620e+05
Rg (reciprocal space) rg_reciprocal20.42 Å
I(0) (reciprocal space) i0_reciprocal21490000.0000
Solution quality estimate total_estimate0.9027
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.5 Å
Skewness Skewness skewness0.185
Kurtosis Kurtosis kurtosis-0.463
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5184000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.992
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ep9a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.78 — ATC-like
Superfamily Superfamily superfamilyc.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family familyc.78.1.1 — Aspartate/ornithine carbamoyltransferase
Domain ID domain_idd1ep9a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.78 — ATC-like
Superfamily Superfamily superfamilyc.78.1 — Aspartate/ornithine carbamoyltransferase
Family Family familyc.78.1.1 — Aspartate/ornithine carbamoyltransferase

CATH v4.4 (2 domains)

Domain ID domain_id1ep9A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1370 — Aspartate/ornithine carbamoyltransferase
Domain ID domain_id1ep9A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1370 — Aspartate/ornithine carbamoyltransferase
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8. Citations (1)

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9. Files and Curves (10)