← Back to search
1l6y

Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid

Method: X-RAY DIFFRACTION Dmax: 86.9 Å Quality: REASONABLE
▼

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

PORPHOBILINOGEN SYNTHASE

Escherichia coli

UniProt P0ACB2

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–323 Chain B； UniProt 1–323 Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 MG MAGNESIUM ION × 8 4OX 4-OXODECANEDIOIC ACID × 8 GOL GLYCEROL × 20 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；PEG 3350, 10% GLYCEROL, 0.1M TRIS-HCL, PH 8.5, 0.02% SODIUM AZIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K Resolution 1.90 Å R-free 0.263

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 1L6Y Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B4E X-ray structure of 5-aminolevulinic acid dehydratase complexed with the inhibitor levulinic acid Deposited 1998-12-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–323（323 aa）
Not recorded SO4 SULFATE ION × 24 ZN ZINC ION × 24 SHF LAEVULINIC ACID × 8 GOL GLYCEROL × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；7MG/ML ENZYME AND 2 - 5 % SATURATED AMMONIUM SULPHATE AS PRECIPITANT. 0.2 M TRIS-HCL USED TO BUFFER THE PH BETWEEN 8.1 AND 8.4. 15MM LEVULINIC ACID, 40UM ZINC SULPHATE AND 4MM BETA- MERCAPTOETHANOL WERE PRESENT., pH 8.2, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.255
1I8J CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID Deposited 2001-03-14 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–323（323 aa）
Chain B 1–323（323 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 8 DSB 4,7-DIOXOSEBACIC ACID × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 3350, GLYCEROL, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.90 Å R-free 0.247
1L6S Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid Deposited 2002-03-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–323（323 aa）
Chain B 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 MG MAGNESIUM ION × 8 DSB 4,7-DIOXOSEBACIC ACID × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；PEG 3350, 10% GLYCEROL, 0.1M TRIS-HCL, PH 8.5, 0.02% SODIUM AZIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.70 Å R-free 0.243
5MHB Product-Complex of E.coli 5-Amino Laevulinic Acid Dehydratase Deposited 2016-11-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–324（324 aa）
Not recorded PBG 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID × 8 ZN ZINC ION × 24 GOL GLYCEROL × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；ALAD at 7 mg per ml mixed with equal volume of well solution: 200 mM Tris pH 8.0 - 8.4, 2 % saturated Ammonium sulphate, 200 microM zinc sulphate, 6 mM beta-mercaptoethanol and 3 mM porphobilinogen. Crystals were grown in the dark.
Resolution 2.10 Å R-free 0.213

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

View Construct and Data Evidence
UniProt name HEM2_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–323； UniProt 1–323 Author chain B； PDBConstruct 1–323； UniProt 1–323

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 1l6y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1l6y
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1l6y
Deposition date deposition_date2002-03-14
Structure title titleCrystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid
Keywords keywordsDEHYDRATASE, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier27.28 Å
Radius of gyration Rg (electron density) rg_electron26.12 Å
Forward intensity I(0) i087363700.00
Molecular weight molecular_weight71429.0 kDa
Excluded volume excluded_volume88613 ų
Envelope volume envelope_volume101500 ų
Hydration-shell volume shell_volume32364 ų
Envelope diameter envelope_diameter96.5 Å
Shell Rg shell_rg33.88 Å
Envelope Rg envelope_rg26.36 Å
Shape Rg shape_rg26.13 Å
Total Rg total_rg26.86 Å
Total atoms total_atoms4988
Residues n_residues644
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
▼

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

Maximum dimension Dmax dmax86.9 Å
Rg (real space) rg_real27.84 Å
Rg uncertainty (real space) rg_real_error0.17 Å
I(0) (real space) i0_real8.6140e+07
I(0) uncertainty (real space) i0_real_error9.3290e+05
Rg (reciprocal space) rg_reciprocal27.30 Å
I(0) (reciprocal space) i0_reciprocal87360000.0000
Solution quality estimate total_estimate0.7028
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.5 Å
Skewness Skewness skewness0.406
Kurtosis Kurtosis kurtosis-0.432
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha5.5280
Highest regularization parameter α highest_alpha27360000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 0.921; Sysdev: 0.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.695
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1l6ya_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.3 — 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)
Domain ID domain_idd1l6yb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.3 — 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)

CATH v4.4 (2 domains)

Domain ID domain_id1l6yA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id1l6yB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
▶

8. Citations (2)

▶

9. Files and Curves (10)