4ox9

Crystal structure of the aminoglycoside resistance methyltransferase NpmA bound to the 30S ribosomal subunit

Method: X-RAY DIFFRACTION

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

30S ribosomal protein S2

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS2_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–256； UniProt 1–256

30S ribosomal protein S3

OrganismNot specified

UniProt P80372

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS3_THET8
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–239； UniProt 1–239

30S ribosomal protein S4

OrganismNot specified

UniProt P80373

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS4_THET8
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–208； UniProt 2–209

30S ribosomal protein S5

OrganismNot specified

UniProt Q5SHQ5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS5_THET8
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–161； UniProt 2–162

30S ribosomal protein S6

OrganismNot specified

UniProt Q5SLP8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS6_THET8
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–101； UniProt 1–101

30S ribosomal protein S7

OrganismNot specified

UniProt P17291

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS7_THET8
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–155； UniProt 2–156

30S ribosomal protein S8

OrganismNot specified

UniProt Q5SHQ2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS8_THET8
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–138； UniProt 1–138

30S ribosomal protein S9

OrganismNot specified

UniProt P80374

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS9_THET8
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 1–128； UniProt 1–128

30S ribosomal protein S10

OrganismNot specified

UniProt Q5SHN7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS10_THET8
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 1–104； UniProt 2–105

30S ribosomal protein S11

OrganismNot specified

UniProt P80376

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS11_THET8
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain K； PDBConstruct 1–129； UniProt 1–129

30S ribosomal protein S12

OrganismNot specified

UniProt Q5SHN3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS12_THET8
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain L； PDBConstruct 1–131； UniProt 1–131

30S ribosomal protein S13

OrganismNot specified

UniProt P80377

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS13_THET8
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain M； PDBConstruct 1–126； UniProt 1–126

30S ribosomal protein S14 type Z

OrganismNot specified

UniProt Q5SHQ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS14Z_THET8
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain N； PDBConstruct 1–60； UniProt 2–61

30S ribosomal protein S15

OrganismNot specified

UniProt Q5SJ76

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS15_THET8
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain O； PDBConstruct 1–88； UniProt 2–89

30S ribosomal protein S16

OrganismNot specified

UniProt Q5SJH3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS16_THET8
Isoform	—
PDB entities	16
Chains and sequence ranges	Author chain P； PDBConstruct 1–88； UniProt 1–88

30S ribosomal protein S17

OrganismNot specified

UniProt Q5SHP7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS17_THET8
Isoform	—
PDB entities	17
Chains and sequence ranges	Author chain Q； PDBConstruct 1–104； UniProt 2–105

30S ribosomal protein S18

OrganismNot specified

UniProt Q5SLQ0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS18_THET8
Isoform	—
PDB entities	18
Chains and sequence ranges	Author chain R； PDBConstruct 1–88； UniProt 1–88

30S ribosomal protein S19

OrganismNot specified

UniProt Q5SHP2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS19_THET8
Isoform	—
PDB entities	19
Chains and sequence ranges	Author chain S； PDBConstruct 1–92； UniProt 2–93

30S ribosomal protein S20

OrganismNot specified

UniProt P80380

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein Thx × 1 （Q5SIH3） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS20_THET8
Isoform	—
PDB entities	20
Chains and sequence ranges	Author chain T； PDBConstruct 1–106； UniProt 1–106

30S ribosomal protein Thx

OrganismNot specified

UniProt Q5SIH3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 16S rRNA (adenine(1408)-N(1))-methyltransferase × 1 （A8C927） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RSHX_THET8
Isoform	—
PDB entities	21
Chains and sequence ranges	Author chain V； PDBConstruct 1–26； UniProt 2–27

16S rRNA (adenine(1408)-N(1))-methyltransferase

Escherichia coli

UniProt A8C927

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 21 RNA 1	16S rRNA × 1 30S ribosomal protein S2 × 1 （P80371） 30S ribosomal protein S3 × 1 （P80372） 30S ribosomal protein S4 × 1 （P80373） 30S ribosomal protein S5 × 1 （Q5SHQ5） 30S ribosomal protein S6 × 1 （Q5SLP8） 30S ribosomal protein S7 × 1 （P17291） 30S ribosomal protein S8 × 1 （Q5SHQ2） 30S ribosomal protein S9 × 1 （P80374） 30S ribosomal protein S10 × 1 （Q5SHN7） 30S ribosomal protein S11 × 1 （P80376） 30S ribosomal protein S12 × 1 （Q5SHN3） 30S ribosomal protein S13 × 1 （P80377） 30S ribosomal protein S14 type Z × 1 （Q5SHQ1） 30S ribosomal protein S15 × 1 （Q5SJ76） 30S ribosomal protein S16 × 1 （Q5SJH3） 30S ribosomal protein S17 × 1 （Q5SHP7） 30S ribosomal protein S18 × 1 （Q5SLQ0） 30S ribosomal protein S19 × 1 （Q5SHP2） 30S ribosomal protein S20 × 1 （P80380） 30S ribosomal protein Thx × 1 （Q5SIH3） MAGNESIUM ION × 120 ZINC ION × 2 SINEFUNGIN × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NPMA_ECOLX
Isoform	—
PDB entities	22
Chains and sequence ranges	Author chain Y； PDBConstruct 4–222； UniProt 1–219

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	4ox9
Deposition date deposition_date	2014-02-04
Structure title title	Crystal structure of the aminoglycoside resistance methyltransferase NpmA bound to the 30S ribosomal subunit
Keywords keywords	;Protein biosynthesis, ribosome, RNA, 30S, 16S, ribosomal subunit, aminoglycoside, A1408, methyltransferase, RIBOSOME-ANTIBIOTIC complex ;; RIBOSOME/ANTIBIOTIC
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.

4ox9__assembly_1__model_1

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

Download this curve (.dat)

4ox9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ox9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	65.85 Å
Rg (electron density)	66.16 Å
Total Rg	66.21 Å
Atom count	53527
Residues	4122
Excluded volume	835170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ox9__assembly_1__model_1`	22-meric （22）	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 (25)

Entity 1 Entity 1 polymer

Description description	16S rRNA
Molecular weight formula_weight	491206.8 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	53527

UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCAC

Entity 2 Entity 2 polymer

Description description	30S ribosomal protein S2
Molecular weight formula_weight	29317.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQEAEATETPEGESEVEA

Entity 3 Entity 3 polymer

Description description	30S ribosomal protein S3
Molecular weight formula_weight	26751.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Entity 4 Entity 4 polymer

Description description	30S ribosomal protein S4
Molecular weight formula_weight	24242.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR

Entity 5 Entity 5 polymer

Description description	30S ribosomal protein S5
Molecular weight formula_weight	17452.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

PETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Entity 6 Entity 6 polymer

Description description	30S ribosomal protein S6
Molecular weight formula_weight	11988.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Entity 7 Entity 7 polymer

Description description	30S ribosomal protein S7
Molecular weight formula_weight	17919.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Entity 8 Entity 8 polymer

Description description	30S ribosomal protein S8
Molecular weight formula_weight	15868.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW

Entity 9 Entity 9 polymer

Description description	30S ribosomal protein S9
Molecular weight formula_weight	14410.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR

Entity 10 Entity 10 polymer

Description description	30S ribosomal protein S10
Molecular weight formula_weight	11823.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

PKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Entity 11 Entity 11 polymer

Description description	30S ribosomal protein S11
Molecular weight formula_weight	13737.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS

Entity 12 Entity 12 polymer

Description description	30S ribosomal protein S12
Molecular weight formula_weight	14508.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAK

Entity 13 Entity 13 polymer

Description description	30S ribosomal protein S13
Molecular weight formula_weight	14338.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK

Entity 14 Entity 14 polymer

Description description	30S ribosomal protein S14 type Z
Molecular weight formula_weight	7027.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW

Entity 15 Entity 15 polymer

Description description	30S ribosomal protein S15
Molecular weight formula_weight	10447.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG

Entity 16 Entity 16 polymer

Description description	30S ribosomal protein S16
Molecular weight formula_weight	10410.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQEAREGA

Entity 17 Entity 17 polymer

Description description	30S ribosomal protein S17
Molecular weight formula_weight	12194.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYESLSKRGGKA

Entity 18 Entity 18 polymer

Description description	30S ribosomal protein S18
Molecular weight formula_weight	10258.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFTEKLVRK

Entity 19 Entity 19 polymer

Description description	30S ribosomal protein S19
Molecular weight formula_weight	10474.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

PRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK

Entity 20 Entity 20 polymer

Description description	30S ribosomal protein S20
Molecular weight formula_weight	11736.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGGLSA

Entity 21 Entity 21 polymer

Description description	30S ribosomal protein Thx
Molecular weight formula_weight	3218.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

GKGDRRTRRGKIWRGTYGKYRPRKKK

Entity 22 Entity 22 polymer

Description description	16S rRNA (adenine(1408)-N(1))-methyltransferase
Molecular weight formula_weight	25197.9 kDa
EC 编号 ec_number	2.1.1.180
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MGSMLILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHVSKH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 23 Entity 23 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	120

Entity 24 Entity 24 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 25 Entity 25 non-polymer

Description description	SINEFUNGIN
Molecular weight formula_weight	381.4 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 26 domains

CATH v4.4 (26 domains)

Domain ID domain_id	4ox9B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	4ox9B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	610 — Helix hairpin bin

Domain ID domain_id	4ox9C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	4ox9C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1140 — Ribosomal protein S3 C-terminal domain
Homologous superfamily homologous superfamily	32 — Ribosomal protein S3, C-terminal domain

Domain ID domain_id	4ox9D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1050 — Ribosomal Protein S4 Delta 41; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Ribosomal protein S4/S9, N-terminal domain

Domain ID domain_id	4ox9D02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily	10 — RNA-binding S4 domain

Domain ID domain_id	4ox9E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4ox9E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4ox9F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	60 — Ribosomal protein S6/Translation elongation factor EF1B

Domain ID domain_id	4ox9G00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	455 — Ribosomal Protein S7
Homologous superfamily homologous superfamily	10 — Ribosomal protein S7/S5

Domain ID domain_id	4ox9H01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4ox9H02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4ox9I00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4ox9J00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	600 — Ribosomal protein S10

Domain ID domain_id	4ox9K00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	80 — Ribosomal protein S11/S14

Domain ID domain_id	4ox9L00
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	4ox9M01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4ox9M02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	910 — 30s ribosomal protein s13; domain 2
Homologous superfamily homologous superfamily	10 — Ribosomal protein S13/S18, C-terminal domain

Domain ID domain_id	4ox9N00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	830 — 30s Ribosomal Protein S14; Chain N
Homologous superfamily homologous superfamily	10 — Ribosomal Protein S14/S29

Domain ID domain_id	4ox9O00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	10 — S15/NS1, RNA-binding

Domain ID domain_id	4ox9P00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1320 — S16 Ribosomal Protein; Chain: A;
Homologous superfamily homologous superfamily	10 — Ribosomal protein S16

Domain ID domain_id	4ox9Q00
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	4ox9R00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	640 — 30s Ribosomal Protein S18
Homologous superfamily homologous superfamily	10 — Ribosomal protein S18

Domain ID domain_id	4ox9S00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	860 — 30s Ribosomal Protein S19; Chain A
Homologous superfamily homologous superfamily	10 — Ribosomal protein S19/S15

Domain ID domain_id	4ox9T00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	110 — Ribosomal protein S20

Domain ID domain_id	4ox9Y00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

▶

Unit-cell length a length_a	403.520 Å
Unit-cell length b length_b	403.520 Å
Unit-cell length c length_c	176.610 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	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.804 Å
Low-resolution limit resolution_low	49.715 Å
R factor r_factor	0.2340
R_work r_work	0.2328
R_free r_free	0.2568

Crystal structure of the aminoglycoside resistance methyltransferase NpmA bound to the 30S ribosomal subunit

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

30S ribosomal protein S2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S11

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer