2iy5

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

Method: X-RAY DIFFRACTION

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

PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 2	PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN × 2 （P27002） TRNAPHE × 2 ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2 MAGNESIUM ION × 2 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYFA_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–350； UniProt 1–350

PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN

OrganismNot specified

UniProt P27002

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 2	PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN × 2 （P27001） TRNAPHE × 2 ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] × 2 MAGNESIUM ION × 2 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYFB_THETH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–785； UniProt 1–785

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_id	2iy5
Deposition date deposition_date	2006-07-12
Structure title title	PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog
Keywords keywords	;CLASS II AMINOACYL-TRNA SYNTHETASE, LIGASE, RBD DOMIN, MAGNESIUM, SH3 DOMAIN, PHENYLALANYL-TRNA SYNTHETASE, THERMUS THERMOPHILUS, PROTEIN BIOSYNTHESIS, METAL-BINDING, NUCLEOTIDE-BINDING, RNA-BINDING, ATP-BINDING, TRNA-BINDING, HELIX-TURN-HELIX MOTIF, AMINOACYL-TRNA SYNTHETASE ;; LIGASE
Experimental Method method	X-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.

2iy5__assembly_1__model_1

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

Download this curve (.dat)

2iy5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2iy5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.16 Å
Rg (electron density)	50.68 Å
Total Rg	51.00 Å
Atom count	20836
Residues	2386
Excluded volume	360230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2iy5__assembly_1__model_1`	hexameric （6）	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)

Entity 1 Entity 1 polymer

Description description	PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN
Molecular weight formula_weight	39309.2 kDa
EC 编号 ec_number	6.1.1.20
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10649

MLEEALAAIQNARDLEELKALKARYLGKKGLLTQEMKGLSALPLEERRKRGQELNAIKAALEAALEAREKALEEAALKEALERERVDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVEGPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTPPFRIVVPGRVFRFEQTDATHEAVFHQLEGLVVGEGIAMAHLKGAIYELAQALFGPDSKVRFQPVYFPFVEPGAQFAVWWPEGGKWLELGGAGMVHPKVFQAVDAYRERLGLPPAYRGVTGFAFGLGVERLAMLRYGIPDIRYFFGGRLKFLEQFKGVL

Entity 2 Entity 2 polymer

Description description	PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN
Molecular weight formula_weight	86736.7 kDa
EC 编号 ec_number	6.1.1.20
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRVPFSWLKAYVPELESPEVLEERLAGLGFETDRIERVFPIPRGVVFARVLEAHPIPGTRLKRLVLDAGRTVEVVSGAENARKGIGVALALPGTELPGLGQKVGERVIQGVRSFGMALSPRELGVGEYGGGLLEFPEDALPPGTPLSEAWPEEVVLDLEVTPNRPDALGLLGLARDLHALGYALVEPEAALKAEALPLPFALKVEDPEGAPHFTLGYAFGLRVAPSPLWMQRALFAAGMRPINNVVDVTNYVMLERAQPMHAFDLRFVGEGIAVRRAREGERLKTLDGVERTLHPEDLVIAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHRFERGVDPLGQVPAQRRALSLLQALAGARVAEALLEAGSPKPPEAIPFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVTPPSHRLDLRLEEDLVEEVARIEGYETIPLALPAFFPAPDNRAVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDARRFRLDPPRLLLLNPLAPEKAALRTHLFPGLVRVLKENLDLDRPERALLFEVGRVFREREETHLAGLLFGEGVGLPWAKERLSGYFLLKGYLEALFARLGLAFRVEAEAFPFLHPGVSGRVLVEGEEVGFLGALHPEIAQELELPPVHLFELRLPLPDKPLAFQDPSRHPAAFRDLAVVVPAPTPYGEVEALVREAAGPYLESLALFDLYQGPPLPEGHKSLAFHLRFRHPKRTLRDEEVEEAVSRVAEALRARGFGLRGLDTP

Entity 3 Entity 3 polymer

Description description	TRNAPHE
Molecular weight formula_weight	24484.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	T

GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE]
Molecular weight formula_weight	480.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	231

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2iy5a1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.7 — tRNA-binding arm
Family Family family	a.2.7.2 — Phenylalanyl-tRNA synthetase (PheRS)

Domain ID domain_id	d2iy5a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Domain ID domain_id	d2iy5b1
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT

Domain ID domain_id	d2iy5b2
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT

Domain ID domain_id	d2iy5b3
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.4 — Myf domain

Domain ID domain_id	d2iy5b4
Class class	b — All beta proteins
Fold Fold fold	b.153 — PheT/TilS domain
Superfamily Superfamily superfamily	b.153.1 — PheT/TilS domain
Family Family family	b.153.1.1 — B3/B4 domain of PheRS, PheT

Domain ID domain_id	d2iy5b5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.13 — Anticodon-binding domain of PheRS
Family Family family	d.58.13.1 — Anticodon-binding domain of PheRS

Domain ID domain_id	d2iy5b6
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

CATH v4.4 (7 domains)

Domain ID domain_id	2iy5A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2iy5B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2iy5B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2iy5B03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
Homologous superfamily homologous superfamily	10 — Phenylalanyl-trna Synthetase, Chain B, domain 3

Domain ID domain_id	2iy5B04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2iy5B05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2iy5B06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	380 — Ferrodoxin-fold anticodon-binding domain

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Unit-cell length a length_a	173.400 Å
Unit-cell length b length_b	173.400 Å
Unit-cell length c length_c	139.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	9.990 Å
R factor r_factor	0.2380
R_work r_work	0.2380
R_free r_free	0.2990

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

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

PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN

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

2iy5__assembly_1__model_1

2iy5__assembly_1__model_1 | I(q)

2iy5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (8 domains)

CATH v4.4 (7 domains)

7. Citations (1)

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

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

PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN

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

2iy5__assembly_1__model_1

2iy5__assembly_1__model_1 | I(q)

2iy5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (8 domains)

CATH v4.4 (7 domains)

7. Citations (1)