2nv2

Structure of the PLP synthase complex Pdx1/2 (YaaD/E) from Bacillus subtilis

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pyridoxal biosynthesis lyase pdxS

Bacillus subtilis

UniProt P37527

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 24 Glutamine amidotransferase subunit pdxT × 12 (P37528) CHLORIDE ION × 12 1,2-ETHANEDIOL × 18 GLUTAMINE × 12 water × 24 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PDXS_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–294; UniProt 0–293 Author chain C; PDBConstruct 1–294; UniProt 0–293 Author chain E; PDBConstruct 1–294; UniProt 0–293 Author chain G; PDBConstruct 1–294; UniProt 0–293 Author chain I; PDBConstruct 1–294; UniProt 0–293 Author chain K; PDBConstruct 1–294; UniProt 0–293 Author chain M; PDBConstruct 1–294; UniProt 0–293 Author chain O; PDBConstruct 1–294; UniProt 0–293 Author chain Q; PDBConstruct 1–294; UniProt 0–293 Author chain S; PDBConstruct 1–294; UniProt 0–293 Author chain U; PDBConstruct 1–294; UniProt 0–293 Author chain W; PDBConstruct 1–294; UniProt 0–293

Glutamine amidotransferase subunit pdxT

Bacillus subtilis

UniProt P37528

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 24 Pyridoxal biosynthesis lyase pdxS × 12 (P37527) CHLORIDE ION × 12 1,2-ETHANEDIOL × 18 GLUTAMINE × 12 water × 24 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PDXT_BACSU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–196; UniProt 1–196 Author chain D; PDBConstruct 1–196; UniProt 1–196 Author chain F; PDBConstruct 1–196; UniProt 1–196 Author chain H; PDBConstruct 1–196; UniProt 1–196 Author chain J; PDBConstruct 1–196; UniProt 1–196 Author chain L; PDBConstruct 1–196; UniProt 1–196 Author chain N; PDBConstruct 1–196; UniProt 1–196 Author chain P; PDBConstruct 1–196; UniProt 1–196 Author chain R; PDBConstruct 1–196; UniProt 1–196 Author chain T; PDBConstruct 1–196; UniProt 1–196 Author chain V; PDBConstruct 1–196; UniProt 1–196 Author chain X; PDBConstruct 1–196; UniProt 1–196

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id2nv2
Deposition date deposition_date2006-11-10
Structure title titleStructure of the PLP synthase complex Pdx1/2 (YaaD/E) from Bacillus subtilis
Keywords keywords(beta/alpha)8-barrel, 3-Layer(aba) Sandwich, PLP synthase complex, LYASE-TRANSFERASE COMPLEX; LYASE/TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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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.

2nv2__assembly_1__model_1

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

Download this curve (.dat)

2nv2__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2nv2__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)59.76 Å
Rg (electron density)59.31 Å
Total Rg59.29 Å
Atom count42086
Residues5554
Excluded volume751780 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2nv2__assembly_1__model_1 24-meric (24) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_idd2nv2a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2c_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2d_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2e_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2f_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2g_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2h_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2i_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2j_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2k_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2l_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2m_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2n_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2o_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2p_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2q_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2r_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2s_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2t_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2u_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2v_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd2nv2w_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.2 — Ribulose-phoshate binding barrel
Family Family familyc.1.2.6 — PdxS-like
Domain ID domain_idd2nv2x_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)

CATH v4.4 (24 domains)

Domain ID domain_id2nv2A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2C00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2E00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2F00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2G00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2H00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2I00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2J00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2K00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2L00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2M00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2N00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2O00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2P00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2Q00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2R00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2S00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2T00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2U00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2V00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id2nv2W00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id2nv2X00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
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7. Citations (1)