3l4g

Crystal structure of Homo Sapiens cytoplasmic Phenylalanyl-tRNA synthetase

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

Phenylalanyl-tRNA synthetase alpha chain

Homo sapiens

UniProt Q9Y285

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Phenylalanyl-tRNA synthetase beta chain × 2 (Q9NSD9) PHENYLALANINE × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Phenylalanyl-tRNA synthetase beta chain × 2 (Q9NSD9) PHENYLALANINE × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Phenylalanyl-tRNA synthetase beta chain × 2 (Q9NSD9) PHENYLALANINE × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Phenylalanyl-tRNA synthetase beta chain × 2 (Q9NSD9) PHENYLALANINE × 2 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name SYFA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–508; UniProt 1–508 Author chain C; PDBConstruct 1–508; UniProt 1–508 Author chain E; PDBConstruct 1–508; UniProt 1–508 Author chain G; PDBConstruct 1–508; UniProt 1–508 Author chain I; PDBConstruct 1–508; UniProt 1–508 Author chain K; PDBConstruct 1–508; UniProt 1–508 Author chain M; PDBConstruct 1–508; UniProt 1–508 Author chain O; PDBConstruct 1–508; UniProt 1–508

Phenylalanyl-tRNA synthetase beta chain

Homo sapiens

UniProt Q9NSD9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Phenylalanyl-tRNA synthetase alpha chain × 2 (Q9Y285) PHENYLALANINE × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Phenylalanyl-tRNA synthetase alpha chain × 2 (Q9Y285) PHENYLALANINE × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Phenylalanyl-tRNA synthetase alpha chain × 2 (Q9Y285) PHENYLALANINE × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Phenylalanyl-tRNA synthetase alpha chain × 2 (Q9Y285) PHENYLALANINE × 2 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name SYFB_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–589; UniProt 1–589 Author chain D; PDBConstruct 1–589; UniProt 1–589 Author chain F; PDBConstruct 1–589; UniProt 1–589 Author chain H; PDBConstruct 1–589; UniProt 1–589 Author chain J; PDBConstruct 1–589; UniProt 1–589 Author chain L; PDBConstruct 1–589; UniProt 1–589 Author chain N; PDBConstruct 1–589; UniProt 1–589 Author chain P; PDBConstruct 1–589; UniProt 1–589

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_id3l4g
Deposition date deposition_date2009-12-20
Structure title titleCrystal structure of Homo Sapiens cytoplasmic Phenylalanyl-tRNA synthetase
Keywords keywords;aminoacylation, tRNA-binding, DNA-binding domain, four-helix bundle, Acetylation, Aminoacyl-tRNA synthetase, ATP-binding, Cytoplasm, Ligase, Nucleotide-binding, Phosphoprotein, Polymorphism, Protein biosynthesis ;; LIGASE
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.

3l4g__assembly_1__model_1

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

Download this curve (.dat)

3l4g__assembly_1__model_1 | I(q)

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

3l4g__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)46.23 Å
Rg (electron density)45.85 Å
Total Rg46.06 Å
Atom count15973
Residues2004
Excluded volume286140 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3l4g__assembly_1__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3l4g__assembly_2__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3l4g__assembly_3__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3l4g__assembly_4__model_1 tetrameric (4) 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 (3)

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6. Fold Classification (SCOP + CATH) 43 domains

CATH v4.4 (43 domains)

Domain ID domain_id3l4gA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gB02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily10 — Phenylalanyl-trna Synthetase, Chain B, domain 3
Domain ID domain_id3l4gB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily240 —
Domain ID domain_id3l4gC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily2320 —
Domain ID domain_id3l4gC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily2330 —
Domain ID domain_id3l4gC04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gD02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily10 — Phenylalanyl-trna Synthetase, Chain B, domain 3
Domain ID domain_id3l4gD03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gD04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gF01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gF02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily10 — Phenylalanyl-trna Synthetase, Chain B, domain 3
Domain ID domain_id3l4gF03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gF04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gH01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gH02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily10 — Phenylalanyl-trna Synthetase, Chain B, domain 3
Domain ID domain_id3l4gH03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gH04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gI01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gJ01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gJ02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily10 — Phenylalanyl-trna Synthetase, Chain B, domain 3
Domain ID domain_id3l4gJ03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gJ04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gK01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gL01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gL02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily10 — Phenylalanyl-trna Synthetase, Chain B, domain 3
Domain ID domain_id3l4gL03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gL04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gM00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gN01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gN02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily10 — Phenylalanyl-trna Synthetase, Chain B, domain 3
Domain ID domain_id3l4gN03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gN04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gO01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id3l4gP01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gP02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily10 — Phenylalanyl-trna Synthetase, Chain B, domain 3
Domain ID domain_id3l4gP03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3l4gP04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
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7. Citations (2)