← Back to search
8a7e

PAPP-A dimer in complex with its inhibitor STC2

Method: ELECTRON MICROSCOPY Dmax: 184.2 Å Quality: GOOD
▼

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

Stanniocalcin-2

Homo sapiens

UniProt O76061

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 44–211 Chain P； UniProt 44–211 Not recorded Pappalysin-1 × 2 （Q13219） ZN ZINC ION × 2 CA CALCIUM ION × 16 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；HEPES buffer 20 mM Hepes pH 7.5 100 mM NaCl, 1mM CaCl cryo-EM vitrification conditions：Cryogen ETHANE；Blot time 4.5 sec Resolution 5.02 Å

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 8A7E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7Y5Q Structure of 1:1 PAPP-A.STC2 complex(half map) Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–302（302 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8A7D Partial dimer complex of PAPP-A and its inhibitor STC2 Deposited 2022-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 44–210（167 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ZN ZINC ION × 1 CA CALCIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Hepes buffer, 20 mM Hepes pH 7.4 100 mM NaCl, 1 mM CaCl
cryo-EM vitrification conditions Cryogen ETHANE；4 s
Resolution 3.06 Å
8HGH Structure of 2:2 PAPP-A.STC2 complex Deposited 2022-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–302（302 aa）
Chain G 1–302（302 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STC2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–168； UniProt 44–211 Author chain P； PDBConstruct 1–168； UniProt 44–211

Pappalysin-1

Homo sapiens

UniProt Q13219

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 82–1617 Chain Q； UniProt 82–1617 Mutation：E563Q Stanniocalcin-2 × 2 （O76061） ZN ZINC ION × 2 CA CALCIUM ION × 16 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；HEPES buffer 20 mM Hepes pH 7.5 100 mM NaCl, 1mM CaCl cryo-EM vitrification conditions：Cryogen ETHANE；Blot time 4.5 sec Resolution 5.02 Å

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 8A7E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7UFG Cryo-EM structure of PAPP-A in complex with IGFBP5 Deposited 2022-03-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 81–1627（1547 aa）
Chain B 81–1627（1547 aa）
Mutation：E483A, S1144Y Mutation：E483A, S1144Y ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 9.2；BTP (Bis-Tris-Propane) pH 9.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7Y5N Structure of 1:1 PAPP-A.ProMBP complex(half map) Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 81–1627（1547 aa）
Chain D 81–1627（1547 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ZN ZINC ION × 1 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
7Y5Q Structure of 1:1 PAPP-A.STC2 complex(half map) Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 81–1627（1547 aa）
Chain B 81–1627（1547 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8A7D Partial dimer complex of PAPP-A and its inhibitor STC2 Deposited 2022-06-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 82–1617（1536 aa）
Chain Q 82–1617（1536 aa）
Mutation：E563Q Mutation：E563Q NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ZN ZINC ION × 1 CA CALCIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Hepes buffer, 20 mM Hepes pH 7.4 100 mM NaCl, 1 mM CaCl
cryo-EM vitrification conditions Cryogen ETHANE；4 s
Resolution 3.06 Å
8D8O Cryo-EM structure of substrate unbound PAPP-A Deposited 2022-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 81–1627（1547 aa）
Chain B 81–1627（1547 aa）
Mutation：E483A, S1144Y Mutation：E483A, S1144Y ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 9.2；BTP (Bis-Tris-Propane) pH 9.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8HGG Structure of 2:2 PAPP-A.ProMBP complex Deposited 2022-11-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–1627（1627 aa）
Chain D 1–1627（1627 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
8HGH Structure of 2:2 PAPP-A.STC2 complex Deposited 2022-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 81–1627（1547 aa）
Chain B 81–1627（1547 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAPP1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–1536； UniProt 82–1617 Author chain Q； PDBConstruct 1–1536； UniProt 82–1617

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 8a7e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8a7e
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8a7e
Deposition date deposition_date2022-06-20
Structure title titlePAPP-A dimer in complex with its inhibitor STC2
Keywords keywordsMetzincin metalloprotease Inhibitor complex, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier56.27 Å
Radius of gyration Rg (electron density) rg_electron55.97 Å
Forward intensity I(0) i02222260000.00
Molecular weight molecular_weight377830.0 kDa
Excluded volume excluded_volume465060 ų
Envelope volume envelope_volume733690 ų
Hydration-shell volume shell_volume109500 ų
Envelope diameter envelope_diameter201.0 Å
Shell Rg shell_rg60.11 Å
Envelope Rg envelope_rg53.42 Å
Shape Rg shape_rg55.96 Å
Total Rg total_rg56.11 Å
Total atoms total_atoms26442
Residues n_residues3384
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 dmax184.2 Å
Rg (real space) rg_real56.03 Å
Rg uncertainty (real space) rg_real_error1.67 Å
I(0) (real space) i0_real2.2220e+09
I(0) uncertainty (real space) i0_real_error4.4020e+07
Rg (reciprocal space) rg_reciprocal56.45 Å
I(0) (reciprocal space) i0_reciprocal2224000000.0000
Solution quality estimate total_estimate0.8812
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary72.4 Å
Skewness Skewness skewness0.139
Kurtosis Kurtosis kurtosis-0.394
Angular range angular_range— – 0.1400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha133200000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.868
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▶

8. Citations (1)

▶

9. Files and Curves (10)