SAXSdb — 9pat

▼

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

6-deoxyerythronolide-B synthase

Amycolatopsis mediterranei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Antibody Fragment 1B2 Heavy Chain × 2 Antibody Fragment 1B2 Light Chain × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O54666_AMYMD
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 32–1580； UniProt 631–2179 Author chain B； PDBConstruct 32–1580； UniProt 631–2179 Author chain C； PDBConstruct 32–1580； UniProt 631–2179

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pat
Deposition date deposition_date	2025-06-25
Structure title title	Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Transacylation Mode
Keywords keywords	Polyketide Synthase Module, Antibody (Fab), Transferase-Immune System complex; Transferase/Immune System
Experimental Method method	ELECTRON MICROSCOPY

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9pat__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9pat__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9pat__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	56.98 Å
Rg (electron density)	56.92 Å
Total Rg	56.94 Å
Atom count	25653
Residues	3464
Excluded volume	453940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9pat__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	6-deoxyerythronolide-B synthase
Molecular weight formula_weight	175359.8 kDa
EC 编号 ec_number	2.3.1.94
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	25653

MASTDSEKVAEYLRRATLDLRAARQRIRELEGEPIAIVGMACRLPGGVASPEDLWRLVAERVDAVSEFPGDRGWDLDSLIDPDRERAGTSYVGQGGFLHDAGEFDAGFFGISPREAVAMDPQQRLLLETSWEALENAGVDPIALKGTDTGVFSGLMGQGYGSGAVAPELEGFVTTGVASSVASGRVSYVLGLEGPAVTVDTACSSSLVAMHLAAQALRQGECSMALAGGVTVMATPGSFVEFSRQRALAPDGRCKAFAAAADGTGWSEGVGVVVLERLSVARERGHRILAVLRGSAVNQDGASNGLTAPNGLSQQRVIRRALAAAGLAPSDVDVVEAHGTGTTLGDPIEAQALLATYGQERKQPLWLGSLKSNIGHAQAAAGVAGVIKMVQALRHETLPPTLHVDKPTLEVDWSAGAIELLTEARAWPRNGRPRRAGVSSFGVSGTNAHLILEEAPAEEPVAAPELPVVPLVVSARSTESLSGQAERLASLLEGDVSLTEVAGALVSRRAVLDERAVVVAGSREEAVTGLRALNTAGSGTPGKVVWVFPGQGTQWAGMGRELLAESPVFAERIAECAAALAPWIDWSLVDVLRGEGDLGRVDVLQPACFAVMVGLAAVWESVGVRPDAVVGHSQGEIAAACVSGALSLEDAAKVVALRSQAIAAELSGRGGMASVALGEDDVVSRLVDGVEVAAVNGPSSVVIAGDAHALDATLEILSGEGIRVRRVAVDYASHTRHVEDIRDTLAETLAGISAQAPAVPFYSTVTSEWVRDAGVLDGGYWYRNLRNQVRFGAAATALLEQGHTVFVEVSAHPVTVQPLSELTGDAIGTLRREDGGLRRLLASMGELFVRGIDVDWTAMVPAAGWVDLPTYAFEHRHYWLEPAEPASAGDPLLGTVVSTPGSDRLTAVAQWSRRAQPWAVDGLVPNAALVEAAIRLGDLAGTPVVGELVVDAPVVLPRRGSREVQLIVGEPGEQRRRPIEVFSREADEPWTRHAHGTLAPAAAAVPEPAAAGDATDVTVAGLRDADRYGIHPALLDAAVRTVVGDDLLPSVWTGVSLLASGATAVTVTPTATGLRLTDPAGQPVLTVESVRGTPFVAEQGTTDALFRVDWPEIPLPTAETADFLPYEATSAEATLSALQAWLADPAETRLAVVTGDCTEPGAAAIWGLVRSAQSEHPGRIVLADLDDPAVLPAVVASGEPQVRVRNGVASVPRLTRVTPRQDARPLDPEGTVLITGGTGTLGALTARHLVTAHGVRHLVLVSRRGEAPELQEELTALGASVAIAACDVADRAQLEAVLRAIPAEHPLTAVIHTAGVLDDGVVTELTPDRLATVRRPKVDAARLLDELTREADLAAFVLFSSAAGVLGNPGQAGYAAANAELDALARQRNSLDLPAVSIAWGYWATVSGMTEHLGDADLRRNQRIGMSGLPADEGMALLDAAIATGGTLVAAKFDVAALRATAKAGGPVPPLLRGLAPLPRRAAAKTASLTERLAGLAETEQAAALLDLVRRHAAEVLGHSGAESVHSGRTFKDAGFDSLTAVELRNRLAAATGLTLSPAMIFDYPKPPALADHLRAKLFGTEVRGEAPSALAGLDALEAALPEVPATEREELVQRLERMLAALRPVAQAADASGTGANPSGDDLGEAGVDELLEALGRELDGDGNSSSVDKLAAALEHHHHHH

Source Source

Source organism organism	Amycolatopsis mediterranei
NCBI taxonomy ID ncbi_taxonomy_id	33910
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	6-deoxyerythronolide-B synthase
Molecular weight formula_weight	175700.2 kDa
EC 编号 ec_number	2.3.1.94
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MASTDSEKVAEYLRRATLDLRAARQRIRELEGEPIAIVGMACRLPGGVASPEDLWRLVAERVDAVSEFPGDRGWDLDSLIDPDRERAGTSYVGQGGFLHDAGEFDAGFFGISPREAVAMDPQQRLLLETSWEALENAGVDPIALKGTDTGVFSGLMGQGYGSGAVAPELEGFVTTGVASSVASGRVSYVLGLEGPAVTVDTACSSSLVAMHLAAQALRQGECSMALAGGVTVMATPGSFVEFSRQRALAPDGRCKAFAAAADGTGWSEGVGVVVLERLSVARERGHRILAVLRGSAVNQDGASNGLTAPNGLSQQRVIRRALAAAGLAPSDVDVVEAHGTGTTLGDPIEAQALLATYGQERKQPLWLGSLKSNIGHAQAAAGVAGVIKMVQALRHETLPPTLHVDKPTLEVDWSAGAIELLTEARAWPRNGRPRRAGVSSFGVSGTNAHLILEEAPAEEPVAAPELPVVPLVVSARSTESLSGQAERLASLLEGDVSLTEVAGALVSRRAVLDERAVVVAGSREEAVTGLRALNTAGSGTPGKVVWVFPGQGTQWAGMGRELLAESPVFAERIAECAAALAPWIDWSLVDVLRGEGDLGRVDVLQPACFAVMVGLAAVWESVGVRPDAVVGHSQGEIAAACVSGALSLEDAAKVVALRSQAIAAELSGRGGMASVALGEDDVVSRLVDGVEVAAVNGPSSVVIAGDAHALDATLEILSGEGIRVRRVAVDYASHTRHVEDIRDTLAETLAGISAQAPAVPFYSTVTSEWVRDAGVLDGGYWYRNLRNQVRFGAAATALLEQGHTVFVEVSAHPVTVQPLSELTGDAIGTLRREDGGLRRLLASMGELFVRGIDVDWTAMVPAAGWVDLPTYAFEHRHYWLEPAEPASAGDPLLGTVVSTPGSDRLTAVAQWSRRAQPWAVDGLVPNAALVEAAIRLGDLAGTPVVGELVVDAPVVLPRRGSREVQLIVGEPGEQRRRPIEVFSREADEPWTRHAHGTLAPAAAAVPEPAAAGDATDVTVAGLRDADRYGIHPALLDAAVRTVVGDDLLPSVWTGVSLLASGATAVTVTPTATGLRLTDPAGQPVLTVESVRGTPFVAEQGTTDALFRVDWPEIPLPTAETADFLPYEATSAEATLSALQAWLADPAETRLAVVTGDCTEPGAAAIWGLVRSAQSEHPGRIVLADLDDPAVLPAVVASGEPQVRVRNGVASVPRLTRVTPRQDARPLDPEGTVLITGGTGTLGALTARHLVTAHGVRHLVLVSRRGEAPELQEELTALGASVAIAACDVADRAQLEAVLRAIPAEHPLTAVIHTAGVLDDGVVTELTPDRLATVRRPKVDAARLLDELTREADLAAFVLFSSAAGVLGNPGQAGYAAANAELDALARQRNSLDLPAVSIAWGYWATVSGMTEHLGDADLRRNQRIGMSGLPADEGMALLDAAIATGGTLVAAKFDVAALRATAKAGGPVPPLLRGLAPLPRRAAAKTASLTERLAGLAETEQAAALLDLVRRHAAEVLGHSGAESVHSGRTFKDAGFDXLTAVELRNRLAAATGLTLSPAMIFDYPKPPALADHLRAKLFGTEVRGEAPSALAGLDALEAALPEVPATEREELVQRLERMLAALRPVAQAADASGTGANPSGDDLGEAGVDELLEALGRELDGDGNSSSVDKLAAALEHHHHHH

Source Source

Source organism organism	Amycolatopsis mediterranei
NCBI taxonomy ID ncbi_taxonomy_id	33910
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Antibody Fragment 1B2 Heavy Chain
Molecular weight formula_weight	26447.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

MAEVQLVQSGGGLVQPGRSLRLSCTASGFTFGDYAMSWVRQAPGKGLEWVGFIRSKAYGGTTEYAASVKGRFTISRDDSKSIAYLQMNSLKTEDTAVYYCTRGGTLFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAALVPRGSAHHHHHHAADYKDDDDKA

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Antibody Fragment 1B2 Light Chain
Molecular weight formula_weight	25715.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,L

LFAIPLVVPFYSHSALDVVMTQSPLSLPVTPGEPASISCRSSQSLLHSNGYNYLDWYLQKPGQSPQLLIYLGSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSLQTPRLTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPRGAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.960 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.96 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	37950

Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Transacylation Mode

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

6-deoxyerythronolide-B synthase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pat__assembly_1__model_1

9pat__assembly_1__model_1 | I(q)

9pat__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)

Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Transacylation Mode

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

6-deoxyerythronolide-B synthase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pat__assembly_1__model_1

9pat__assembly_1__model_1 | I(q)

9pat__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)