2rhs

PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies

Method: X-RAY DIFFRACTION

▼

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

Phenylalanyl-tRNA synthetase alpha chain

Staphylococcus haemolyticus

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 （Q4L5E4） 1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea × 2 SULFATE ION × 2 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYFA_STAHJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 27–294； UniProt 84–351 Author chain C； PDBConstruct 27–294； UniProt 84–351

Phenylalanyl-tRNA synthetase beta chain

Staphylococcus haemolyticus

UniProt Q4L5E4

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 （Q4L5E3） 1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea × 2 SULFATE ION × 2 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYFB_STAHJ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–800； UniProt 1–800 Author chain D； PDBConstruct 1–800； UniProt 1–800

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	2rhs
Deposition date deposition_date	2007-10-09
Structure title title	PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies
Keywords keywords	;heterotetramer, phenylalanine, tRNA, Aminoacyl-tRNA synthetase, ATP-binding, Cytoplasm, Ligase, Magnesium, Metal-binding, Nucleotide-binding, Protein biosynthesis, RNA-binding, tRNA-binding ;; LIGASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2rhs__assembly_1__model_1

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

Download this curve (.dat)

2rhs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rhs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.79 Å
Rg (electron density)	48.72 Å
Total Rg	48.83 Å
Atom count	16482
Residues	2091
Excluded volume	292740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rhs__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Phenylalanyl-tRNA synthetase alpha chain
Molecular weight formula_weight	33395.8 kDa
EC 编号 ec_number	6.1.1.20
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	17461

MGSSHHHHHHSSGLVPRGSHMGTELMEKLNQQLAEETIDVTLPSRQISIGSKHPLTRTVEEIEDLFLGLGYEIVDGYEVEQDYYNFEALNLPKSHPARDMQDSFYITDEILMRTHTSPVQARTMEKRNGQGPVKIICPGKVYRRDSDDATHSHQFTQIEGLVVDKNIKMSDLKGTLELVAKKLFGADREIRLRPSYFPFTEPSVEVDVSCFKCKGKGCNVCKHTGWIEILGAGMVHPNVLEMAGFDSNEYSGFAFGMGPDRIAMLKYGIEDIRYFYTNDVRFLEQFKAVEDRGE

Source Source

Source organism organism	Staphylococcus haemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	1283
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Phenylalanyl-tRNA synthetase beta chain
Molecular weight formula_weight	88753.9 kDa
EC 编号 ec_number	6.1.1.20
Mutation mutation	D34N, Q144P, E661G, Q663A, D664G
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MLISNEWLKDYVDAGVKVEDLAERITRTGIEVDNMIDYSKDIKNLVVGYIQSKEKHPDADKLNICQVDIGEEEPVQIVCGAPNVDAGQHVIVAKVGGRLPGGIKIKRAKLRGERSEGMICSLQEIGISSNVVPKAYENGIFVFPTEVEPGTDALTALYLNDQVMEFDLTPNRADALSMVGTAYEVAALYQTEMTKPETQSNETSESATNELSVTIDNPEKVPYYSARVVKNVSIEPSPIWVQARLIKAGIRPINNVVDISNYVLLEYGQPLHMFDQDHIGSKEIVVRQAKDEETMTTLDNNERKLVDTDIVISNGQEPIALAGVMGGDFSEVTEQTTNVVIEGAIFDPVSIRHTSRRLNLRSEASSRFEKGIATEFVDEAVDRACYLLQELASGEVLQDRVSSGDLGSFVTPIDITAEKVNKTIGFNLSNDEIQSIFRQLGFETTLKGETLTVNVPSRRKDITIKEDLIEEVARIYGYDEIPSSLPVFGEVTSGELTDRQHKTRTLKETLEGAGLNQAITYSLVSKDHAKDFALQERPTISLLMPMSEAHATLRQSLLPHLIEATAYNVARKNKDVRLYEIGRVFFGNGEGELPDEVEYLSGILTGEYVVNAWQGKKEEIDFFIAKGVVDRVAEKLNLEFSYKAGKIEGLHPGRTAIVSLGGAGIGFIGELHPQVAADNDLKRTYVFELNYDAMMQVAVGYINYEQIPKFPGVTRDIALEVNHDVPSSELKQIIHNNGEDILQSTLVFDVYEGEHLEKGKKSVAIRLNYLDTEDTLTDERVSKIHDKILEALQAQGATIR

Source Source

Source organism organism	Staphylococcus haemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	1283
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea
Molecular weight formula_weight	444.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 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	946

▼

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2rhsa_
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.104.1.0 — automated matches

Domain ID domain_id	d2rhsc1
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.104.1.0 — automated matches

Domain ID domain_id	d2rhsc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (14 domains)

Domain ID domain_id	2rhsA01
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	2rhsB01
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	2rhsB02
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	2rhsB03
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	2rhsB04
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	2rhsB05
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	2rhsB06
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

Domain ID domain_id	2rhsC00
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	2rhsD01
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	2rhsD02
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	2rhsD03
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	2rhsD04
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	2rhsD05
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	2rhsD06
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

▶

Unit-cell length a length_a	60.714 Å
Unit-cell length b length_b	87.861 Å
Unit-cell length c length_c	234.036 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	57.300 Å
R factor r_factor	0.1970
R_work r_work	0.1930
R_free r_free	0.2710

PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies

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

2rhs__assembly_1__model_1

2rhs__assembly_1__model_1 | I(q)

2rhs__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (3 domains)

CATH v4.4 (14 domains)

7. Citations (1)

PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies

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

2rhs__assembly_1__model_1

2rhs__assembly_1__model_1 | I(q)

2rhs__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (3 domains)

CATH v4.4 (14 domains)

7. Citations (1)