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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

Method: SOLUTION NMR Dmax: 47.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Erythronolide synthase

Saccharopolyspora erythraea

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 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 3490–3547 Chain B； UniProt 3490–3547 Fragment：C-terminal fragment Mutation：L1G, F2S No other associated polymer 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

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 1PZQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11SZ Antibody (1B2) Bound Rifamycin Synthetase Module 2 Deposited 2026-03-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 3489–3567（79 aa）
Chain B 3489–3567（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
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 mutation/modification Different oligomeric state 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 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions 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 method 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 method 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 3–60； UniProt 3490–3547 Author chain B； PDBConstruct 3–60； UniProt 3490–3547

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 1pzq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1pzq
Deposition date deposition_date2003-07-14
Structure title titleStructure of fused docking domains from the erythromycin polyketide synthase (DEBS), a model for the interaction between DEBS 2 and DEBS 3: The A domain
Keywords keywordsFOUR HELIX BUNDLE, HOMODIMER, TRANSFERASE; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.28 Å
Radius of gyration Rg (electron density) rg_electron16.50 Å
Forward intensity I(0) i0194260000.00
Molecular weight molecular_weight102620.0 kDa
Excluded volume excluded_volume123450 ų
Envelope volume envelope_volume47545 ų
Hydration-shell volume shell_volume18765 ų
Envelope diameter envelope_diameter86.6 Å
Shell Rg shell_rg28.27 Å
Envelope Rg envelope_rg23.85 Å
Shape Rg shape_rg16.49 Å
Total Rg total_rg17.10 Å
Total atoms total_atoms14064
Residues n_residues960
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 dmax47.9 Å
Rg (real space) rg_real16.11 Å
Rg uncertainty (real space) rg_real_error0.09 Å
I(0) (real space) i0_real1.8540e+08
I(0) uncertainty (real space) i0_real_error1.7920e+06
Rg (reciprocal space) rg_reciprocal17.54 Å
I(0) (reciprocal space) i0_reciprocal194300000.0000
Solution quality estimate total_estimate0.6713
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.0 Å
Skewness Skewness skewness0.464
Kurtosis Kurtosis kurtosis-0.194
Angular range angular_range— – 0.4600 Å−1
Current regularization parameter α current_alpha2.5290
Highest regularization parameter α highest_alpha909100.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.009; Oscil: 0.920; Stabil: 0.992; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1pzqa1
Class classa — All alpha proteins
Fold Fold folda.34 — Dimerisation interlock
Superfamily Superfamily superfamilya.34.3 — Docking domain A of the erythromycin polyketide synthase (DEBS)
Family Family familya.34.3.1 — Docking domain A of the erythromycin polyketide synthase (DEBS)
Domain ID domain_idd1pzqa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1pzqb1
Class classa — All alpha proteins
Fold Fold folda.34 — Dimerisation interlock
Superfamily Superfamily superfamilya.34.3 — Docking domain A of the erythromycin polyketide synthase (DEBS)
Family Family familya.34.3.1 — Docking domain A of the erythromycin polyketide synthase (DEBS)
Domain ID domain_idd1pzqb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id1pzqA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1140 — Docking domain of the erythromycin polyketide synthase (DEBS)
Domain ID domain_id1pzqB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1140 — Docking domain of the erythromycin polyketide synthase (DEBS)
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8. Citations (1)

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9. Files and Curves (10)