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11sz

Antibody (1B2) Bound Rifamycin Synthetase Module 2

Method: ELECTRON MICROSCOPY Dmax: 187.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

6-deoxyerythronolide-B synthase, Erythronolide synthase EryA2

Amycolatopsis mediterranei

UniProt O54666

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 2194–3157 Chain B； UniProt 2194–3157 Not recorded 1B2 Antibody Fragment (Fab) Heavy Chain × 2 1B2 Antibody Fragment (Fab) Light Chain × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 11SZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9PAT Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Transacylation Mode Deposited 2025-06-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 631–2179（1549 aa）
Chain B 631–2179（1549 aa）
Chain C 631–2179（1549 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH)
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
9PAV Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Elongation Mode Deposited 2025-06-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 631–2179（1549 aa）
Chain B 631–2179（1549 aa）
Chain C 631–2179（1549 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH)
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
9PC6 Antibody (1B2) Bound Crosslinked Rifamycin Synthetase Module 1 with a C-terminal Type II Thioesterase Deposited 2025-06-27 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 631–2180（1550 aa）
Chain B 631–2180（1550 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 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH)
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å

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

View Construct and Data Evidence
UniProt name O54666_AMYMD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 32–995； UniProt 2194–3157 Author chain B； PDBConstruct 32–995； UniProt 2194–3157

6-deoxyerythronolide-B synthase, Erythronolide synthase EryA2

Amycolatopsis mediterranei

UniProt Q03132

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 3489–3567 Chain B； UniProt 3489–3567 Not recorded 1B2 Antibody Fragment (Fab) Heavy Chain × 2 1B2 Antibody Fragment (Fab) Light Chain × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 11SZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1PZQ Structure of fused docking domains from the erythromycin polyketide synthase (DEBS), a model for the interaction between DEBS 2 and DEBS 3: The A domain Deposited 2003-07-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3490–3547（58 aa） Fragment：C-terminal fragment
Chain B 3490–3547（58 aa） Fragment：C-terminal fragment
Mutation：L1G, F2S Mutation：L1G, F2S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer NA；Pressure ambient
NMR sample composition 1mM DOCK23 U-15N,13C: 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM DOCK23 (50% U-15N,13C: 50% unlabeled): 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
1PZR Structure of fused docking domains from the erythromycin polyketide synthase (DEBS), a model for the interaction between DEBS2 and DEBS3: the B domain Deposited 2003-07-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3548–3567（20 aa） Fragment：RESIDUES 61-120
Chain B 3548–3567（20 aa） Fragment：RESIDUES 61-120
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer NA；Pressure ambient
NMR sample composition 1mM DOCK23 U-15N,13C: 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM DOCK23 (50% U-15N,13C: 50% unlabeled): 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3EL6 Crystal Structure of the Erythromycin Dehydratase Deposited 2008-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2362–2653（292 aa） Fragment：EryDH4 (UNP residues 2362 to 2653)
Not recorded SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；295 K；2.15 M ammonium sulfate, 100 mM sodium cacodylate pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.85 Å R-free 0.227
6C9U Crystal structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase in complex with antibody fragment (Fab) Deposited 2018-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–922（921 aa） Fragment：[KS3][AT3] didomain from module 3
Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 2 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；200 mM potassium citrate, 20%(w/v) PEG 3,350 and 12% ethylene glycol)
Resolution 2.09 Å R-free 0.210
7M7E 6-Deoxyerythronolide B synthase (DEBS) hybrid module (M3/1) in complex with antibody fragment 1B2 Deposited 2021-03-28 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–922（921 aa） Fragment：EryA2 (UNP residues 2-922) + EryA1 (UNP residues 1457-2015) + EryA3 (UNP residues 2896-3172)
Chain B 2–922（921 aa） Fragment：EryA2 (UNP residues 2-922) + EryA1 (UNP residues 1457-2015) + EryA3 (UNP residues 2896-3172)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7S6C CryoEM structure of modular PKS holo-Lsd14 stalled at the condensation step and bound to antibody fragment 1B2, composite structure Deposited 2021-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain A 2–30（29 aa）
Chain B 2–30（29 aa）
Chain C 2–30（29 aa）
Chain D 2–30（29 aa）
Not recorded ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 5 seconds before plunging in liquid ethane.
Resolution 3.10 Å
7S6D CryoEM structure of modular PKS holo-Lsd14 bound to antibody fragment 1B2, composite structure Deposited 2021-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 2–30（29 aa）
Chain B 2–30（29 aa）
Chain C 2–30（29 aa）
Not recorded ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 5 seconds before plunging in liquid ethane.
Resolution 3.10 Å

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

View Construct and Data Evidence
UniProt name ERYA2_SACER
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 996–1074； UniProt 3489–3567 Author chain B； PDBConstruct 996–1074； UniProt 3489–3567

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 11sz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 11sz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id11sz
Deposition date deposition_date2026-03-11
Structure title titleAntibody (1B2) Bound Rifamycin Synthetase Module 2
Keywords keywordspolyketide synthase, antibody, BIOSYNTHETIC PROTEIN-Immune System complex; BIOSYNTHETIC PROTEIN/Immune System
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier50.25 Å
Radius of gyration Rg (electron density) rg_electron50.60 Å
Forward intensity I(0) i0773818000.00
Molecular weight molecular_weight223610.0 kDa
Excluded volume excluded_volume277650 ų
Envelope volume envelope_volume412720 ų
Hydration-shell volume shell_volume73493 ų
Envelope diameter envelope_diameter195.3 Å
Shell Rg shell_rg48.87 Å
Envelope Rg envelope_rg50.16 Å
Shape Rg shape_rg50.57 Å
Total Rg total_rg50.62 Å
Total atoms total_atoms15743
Residues n_residues2115
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 dmax187.2 Å
Rg (real space) rg_real50.51 Å
Rg uncertainty (real space) rg_real_error2.50 Å
I(0) (real space) i0_real7.7380e+08
I(0) uncertainty (real space) i0_real_error1.6510e+07
Rg (reciprocal space) rg_reciprocal50.04 Å
I(0) (reciprocal space) i0_reciprocal773300000.0000
Solution quality estimate total_estimate0.7913
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary66.4 Å
Skewness Skewness skewness0.605
Kurtosis Kurtosis kurtosis0.491
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha82770000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.585; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.851; Smooth: 0.676
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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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8. Citations (1)

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9. Files and Curves (10)