SAXSdb — 1j5a

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

RIBOSOMAL PROTEIN L4

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 1	23S RRNA × 1 RIBOSOMAL PROTEIN L22 × 1 （Q9RXJ7） RIBOSOMAL PROTEIN L32 × 1 （P49228） CLARITHROMYCIN × 1 MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL4_DEIRA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain K； PDBConstruct 1–205； UniProt 1–205

RIBOSOMAL PROTEIN L22

OrganismNot specified

UniProt Q9RXJ7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 1	23S RRNA × 1 RIBOSOMAL PROTEIN L4 × 1 （Q9RXK1） RIBOSOMAL PROTEIN L32 × 1 （P49228） CLARITHROMYCIN × 1 MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL22_DEIRA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain L； PDBConstruct 1–134； UniProt 1–134

RIBOSOMAL PROTEIN L32

OrganismNot specified

UniProt P49228

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 1	23S RRNA × 1 RIBOSOMAL PROTEIN L4 × 1 （Q9RXK1） RIBOSOMAL PROTEIN L22 × 1 （Q9RXJ7） CLARITHROMYCIN × 1 MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL32_DEIRA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain M； PDBConstruct 1–60； UniProt 1–60

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	1j5a
Deposition date deposition_date	2002-03-06
Structure title title	STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA
Keywords keywords	RIBOSOME, 50S, 23S, 5S, ANTIBIOTICS, CLARITHROMYCIN, PEPTIDYL TRANSFERASE CENTER; RIBOSOME
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.

1j5a__assembly_1__model_1

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

Download this curve (.dat)

1j5a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1j5a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	64.95 Å
Rg (electron density)	64.49 Å
Total Rg	64.56 Å
Atom count	59586
Residues	2774
Excluded volume	892960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1j5a__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	23S RRNA
Molecular weight formula_weight	933405.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	59971

GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC

Entity 2 Entity 2 polymer

Description description	RIBOSOMAL PROTEIN L4
Molecular weight formula_weight	22308.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDAAALEIVEEEAGEEQQ

Entity 3 Entity 3 polymer

Description description	RIBOSOMAL PROTEIN L22
Molecular weight formula_weight	15190.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MTAPEQTFRNKKQRKQQVKLRKPGFAVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLLRFIPRSASEPVAKVLNSAKANALHNDEMLEDRLFVKEAYVDAGPTLKRLIPRARGSANIIKKRTSHITIIVAEKGNK

Entity 4 Entity 4 polymer

Description description	RIBOSOMAL PROTEIN L32
Molecular weight formula_weight	6810.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MAKHPVPKKKTSKSKRDMRRSHHALTAPNLTECPQCHGKKLSHHICPNCGYYDGRQVLAV

Entity 5 Entity 5 non-polymer

Description description	CLARITHROMYCIN
Molecular weight formula_weight	748.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1j5ak_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d1j5al_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d1j5am_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

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Unit-cell length a length_a	169.900 Å
Unit-cell length b length_b	412.700 Å
Unit-cell length c length_c	697.000 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2780
R_work r_work	0.2730
R_free r_free	0.3230

STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA

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

RIBOSOMAL PROTEIN L4

State in the Current Structure

Other States of the Same Protein in the Database

RIBOSOMAL PROTEIN L22

State in the Current Structure

Other States of the Same Protein in the Database

RIBOSOMAL PROTEIN L32

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

1j5a__assembly_1__model_1

1j5a__assembly_1__model_1 | I(q)

1j5a__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 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)

STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA

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

RIBOSOMAL PROTEIN L4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RIBOSOMAL PROTEIN L22

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RIBOSOMAL PROTEIN L32

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

1j5a__assembly_1__model_1

1j5a__assembly_1__model_1 | I(q)

1j5a__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 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)