Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin
DeMirci, H.To be published.
Experimental Data Snapshot
wwPDB Validation 3D Report Full Report
Find similar proteins by: Sequence  |  Structure
Entity ID: 2 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S2 | B | 234 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsB (rps2) |
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80371 |
Entity ID: 3 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S3 | C | 206 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsC (rps3) |
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80372 |
Entity ID: 4 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S4 | D | 208 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsD (rps4) |
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80373 |
Entity ID: 5 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
RIBOSOMAL PROTEIN S5 | E | 150 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsE |
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHQ5 |
Entity ID: 6 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S6 | F | 101 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsF |
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SLP8 |
Entity ID: 7 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S7 | G | 155 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsG (rps7) |
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P17291 |
Entity ID: 8 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S8 | H | 138 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsH |
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P0DOY9 |
Entity ID: 9 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S9 | I | 127 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsI (rps9) |
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80374 |
Entity ID: 10 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S10 | J | 98 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsJ |
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHN7 |
Entity ID: 11 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S11 | K | 116 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsK (rps11) |
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80376 |
Entity ID: 12 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S12 | L | 124 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsL |
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHN3 |
Entity ID: 13 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S13 | M | 118 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsM (rps13) |
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80377 |
Entity ID: 14 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S14 type Z | N | 60 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsZ (rpsN) |
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P0DOY6 |
Entity ID: 15 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S15 | O | 87 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsO |
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SJ76 |
Entity ID: 16 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S16 | P | 83 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsP |
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SJH3 |
Entity ID: 17 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S17 | Q | 99 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsQ |
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P0DOY7 |
Entity ID: 18 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S18 | R | 70 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsR |
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SLQ0 |
Entity ID: 19 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S19 | S | 80 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsS |
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHP2 |
Entity ID: 20 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein S20 | T | 99 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsT (rps20) |
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80380 |
Entity ID: 21 | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details |
30S ribosomal protein Thx | U | 24 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0  Gene Names: rpsU |
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SIH3 |
Entity ID: 1 | ||||
---|---|---|---|---|
Molecule | Chains | Length | Organism | |
16S Ribosomal RNA rRNA | A | 1522 | Thermus thermophilus HB8 |
Entity ID: 22 | ||||
---|---|---|---|---|
Molecule | Chains | Length | Organism | |
RNA (5'-R(*UP*UP*UP*UP*UP*U)-3') | Y | 6 | Thermus thermophilus HB8 |
Entity ID: 23 | ||||
---|---|---|---|---|
Molecule | Chains | Length | Organism | |
RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3') | W | 15 | Thermus thermophilus HB8 |
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
ZN Query on ZN | D, N | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | ![]() |  Ligand Interaction | |
MG Query on MG | A, B, C, D, E, F, H, K, L, M, P, Q, S, T, W | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | ![]() |  Ligand Interaction | |
SIS Query on SIS | A | (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside Sisomicin C19 H37 N5 O7 URWAJWIAIPFPJE-YFMIWBNJSA-N | ![]() |  Ligand Interaction |
Modified Residues  9 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
PSU Query on PSU | A | RNA LINKING | C9 H13 N2 O9 P | ![]() | U |
5MC Query on 5MC | A | RNA LINKING | C10 H16 N3 O8 P | ![]() | C |
M2G Query on M2G | A | RNA LINKING | C12 H18 N5 O8 P | ![]() | G |
MA6 Query on MA6 | A | RNA LINKING | C12 H18 N5 O7 P | ![]() | A |
2MG Query on 2MG | A | RNA LINKING | C11 H16 N5 O8 P | ![]() | G |
G7M Query on G7M | A | RNA LINKING | C11 H17 N5 O8 P | ![]() | G |
UR3 Query on UR3 | A | RNA LINKING | C10 H15 N2 O9 P | ![]() | U |
0TD Query on 0TD | L | L-PEPTIDE LINKING | C5 H9 N O4 S | ![]() | ASP |
4OC Query on 4OC | A | RNA LINKING | C11 H18 N3 O8 P | ![]() | C |
Length (Å) | Angle (°) |
---|---|
a = 400.970 | α = 90.00 |
b = 400.970 | β = 90.00 |
c = 175.050 | γ = 90.00 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
PDB_EXTRACT | data extraction |
PHENIX | phasing |
XSCALE | data scaling |