4KHP image
Deposition Date 2013-05-01
Release Date 2013-06-05
Last Version Date 2024-11-06
Entry Detail
PDB ID:
4KHP
Keywords:
RIBOSOME/ANTIBIOTIC
Title:
Structure of the Thermus thermophilus 30S ribosomal subunit in complex with de-6-MSA-pactamycin
Biological Source:
Source Organism:
Thermus thermophilus (Taxon ID: 300852)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.10 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 41 21 2
4KHP validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:A
Chain Length:1506
Number of Molecules:1
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B
Chain Length:234
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80371 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E
Chain Length:150
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP8 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G
Chain Length:155
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P17291 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S8
Chain IDs:H
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I
Chain Length:127
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80374 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J
Chain Length:98
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN7 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80376 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L
Chain Length:125
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M
Chain Length:120
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80377 Pfam ID:PF00416
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S14
Chain IDs:N
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJ76 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P
Chain Length:83
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJH3 Pfam ID:PF00886
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S17
Chain IDs:Q
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S
Chain Length:78
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80380 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S Ribosomal protein THX
Gene (Uniprot):rpsU
Chain IDs:U
Chain Length:24
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:Fragment of messenger RNA
Chain IDs:V (auth: X)
Chain Length:6
Number of Molecules:1
Biological Source:Thermus thermophilus
Ligand Molecules
MG
PAR
PCY
Primary Citation
Crystal Structure of a Bioactive Pactamycin Analog Bound to the 30S Ribosomal Subunit.
J.Mol.Biol. 425 3907 3910 (2013)
PMID: 23702293 DOI: 10.1016/j.jmb.2013.05.004

Abstact

Biosynthetically and chemically derived analogs of the antibiotic pactamycin and de-6-methylsalicylyl (MSA)-pactamycin have attracted recent interest as potential antiprotozoal and antitumor drugs. Here, we report a 3.1-Å crystal structure of de-6-MSA-pactamycin bound to its target site on the Thermus thermophilus 30S ribosomal subunit. Although de-6-MSA-pactamycin lacks the MSA moiety, it shares the same binding site as pactamycin and induces a displacement of nucleic acid template bound at the E-site of the 30S. The structure highlights unique interactions between this pactamycin analog and the ribosome, which paves the way for therapeutic development of related compounds.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
1HNX