1hc7

Prolyl-tRNA synthetase from Thermus thermophilus

Method: X-RAY DIFFRACTION

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein homooligomer	Homooligomer	2 / 0 / 0 / 0	Consistent with protein count
2	Protein homooligomer	Homooligomer	2 / 0 / 0 / 0	Consistent with protein count

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	1hc7
Deposition date deposition_date	2001-04-26
Structure title title	Prolyl-tRNA synthetase from Thermus thermophilus
Keywords keywords	AMINOACYL-TRNA SYNTHETASE, ATP + L-PROLINE + TRNA(PRO) AMP + PPI + L-PROLYL-TRNA(PRO), CLASS II AMINOACYL-TRNA SYNTHETASE; AMINOACYL-TRNA SYNTHETASE
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.

1hc7__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1hc7__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1hc7__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.27 Å
Rg (electron density)	30.04 Å
Total Rg	30.91 Å
Atom count	7430
Residues	928
Excluded volume	132040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1hc7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1hc7__assembly_2__model_1`	dimeric （2）	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)

Entity 1 Entity 1 polymer

Description description	PROLYL-TRNA SYNTHETASE
Molecular weight formula_weight	54563.0 kDa
EC 编号 ec_number	6.1.1.15
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15730

MAKEKGLTPQSQDFSEWYLEVIQKAELADYGPVRGTIVVRPYGYAIWENIQQVLDRMFKETGHQNAYFPLFIPMSFLRKEAEHVEGFSPELAVVTHAGGEELEEPLAVRPTSETVIGYMWSKWIRSWRDLPQLLNQWGNVVRWEMRTRPFLRTSEFLWQEGHTAHATREEAEEEVRRMLSIYARLAREYAAIPVIEGLKTEKEKFAGAVYTTTIEALMKDGKALQAGTSHYLGENFARAFDIKFQDRDLQVKYVHTTSWGLSWRFIGAIIMTHGDDRGLVLPPRLAPIQVVIVPIYKDESRERVLEAAQGLRQALLAQGLRVHLDDRDQHTPGYKFHEWELKGVPFRVELGPKDLEGGQAVLASRLGGKETLPLAALPEALPGKLDAFHEELYRRALAFREDHTRKVDTYEAFKEAVQEGFALAFHCGDKACERLIQEETTATTRCVPFEAEPEEGFCVRCGRPSAYGKRVVFAKAY

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	738

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1hc7a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1hc7a2
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	d1hc7a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.5 — C-terminal domain of ProRS
Family Family family	d.68.5.1 — C-terminal domain of ProRS

Domain ID domain_id	d1hc7b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1hc7b2
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	d1hc7b3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.5 — C-terminal domain of ProRS
Family Family family	d.68.5.1 — C-terminal domain of ProRS

Domain ID domain_id	d1hc7c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1hc7c2
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	d1hc7c3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.5 — C-terminal domain of ProRS
Family Family family	d.68.5.1 — C-terminal domain of ProRS

Domain ID domain_id	d1hc7d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1hc7d2
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	d1hc7d3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.5 — C-terminal domain of ProRS
Family Family family	d.68.5.1 — C-terminal domain of ProRS

CATH v4.4 (12 domains)

Domain ID domain_id	1hc7A01
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	1hc7A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	1hc7A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

Domain ID domain_id	1hc7B01
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	1hc7B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	1hc7B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

Domain ID domain_id	1hc7C01
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	1hc7C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	1hc7C03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

Domain ID domain_id	1hc7D01
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	1hc7D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	1hc7D03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

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Unit-cell length a length_a	132.300 Å
Unit-cell length b length_b	191.100 Å
Unit-cell length c length_c	125.100 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.430 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2340