National Center for
Biotechnology Information

5OBM: Crystal structure of Gentamicin bound to the yeast 80S ribosome

PDB ID:	5OBM Download
MMDB ID:	171330
PDB Deposition Date:	2017/6/28
Updated in MMDB:	2024/05
Experimental Method:	x-ray diffraction
Resolution:	3.4 Å
Source Organism:	Saccharomyces cerevisiae S288C
Similar Structures:

Biological Unit for 5OBM: 79-meric; determined by author

Molecular Components in 5OBM
Label	Count	Molecule
Proteins (75 molecules)
L2	1	60S Ribosomal Protein L2-a
L3	1	60S Ribosomal Protein L3
L4	1	60S Ribosomal Protein L4-a
L5	1	60S Ribosomal Protein L5
L6	1	60S Ribosomal Protein L6-a
L7	1	60S Ribosomal Protein L7-a
L8	1	60S Ribosomal Protein L8-a
L9	1	60S Ribosomal Protein L9-a
M0	1	60S Ribosomal Protein L10
M1	1	60S Ribosomal Protein L11-b
M3	1	60S Ribosomal Protein L13-a
M4	1	60S Ribosomal Protein L14-a
M5	1	60S Ribosomal Protein L15-a
M6	1	60S Ribosomal Protein L16-a
M7	1	60S Ribosomal Protein L17-a
M8	1	60S Ribosomal Protein L18-a
M9	1	60S Ribosomal Protein L19-a
N0	1	60S Ribosomal Protein L20-a
N1	1	60S Ribosomal Protein L21-a
N2	1	60S Ribosomal Protein L22-a
N3	1	60S Ribosomal Protein L23-a
N4	1	60S Ribosomal Protein L24-a
N5	1	60S Ribosomal Protein L25
N6	1	60S Ribosomal Protein L26-a
N7	1	60S Ribosomal Protein L27-a
N8	1	60S Ribosomal Protein L28
N9	1	60S Ribosomal Protein L29
O0	1	60S Ribosomal Protein L30
O1	1	60S Ribosomal Protein L31-a
O2	1	60S Ribosomal Protein L32
O3	1	60S Ribosomal Protein L33-a
O4	1	60S Ribosomal Protein L34-a
O5	1	60S Ribosomal Protein L35-a
O6	1	60S Ribosomal Protein L36-a
O7	1	60S Ribosomal Protein L37-a
O8	1	60S Ribosomal Protein L38
O9	1	60S Ribosomal Protein L39
Q0	1	Ubiquitin-60s Ribosomal Protein L40
Q1	1	60S Ribosomal Protein L41-a
Q2	1	60S Ribosomal Protein L42-a
Q3	1	60S Ribosomal Protein L43-a
S0	1	40S Ribosomal Protein S0-a
S1	1	40S Ribosomal Protein S1-a
S2	1	40S Ribosomal Protein S2
S3	1	40S Ribosomal Protein S3
S4	1	40S Ribosomal Protein S4-a
S5	1	40S Ribosomal Protein S5
S6	1	40S Ribosomal Protein S6-a
S7	1	40S Ribosomal Protein S7-a
S8	1	40S Ribosomal Protein S8-a
S9	1	40S Ribosomal Protein S9-a
C0	1	40S Ribosomal Protein S10-a
C1	1	40S Ribosomal Protein S11-a
C2	1	40S Ribosomal Protein S12
C3	1	40S Ribosomal Protein S13
C4	1	40S Ribosomal Protein S14-b
C5	1	40S Ribosomal Protein S15
C6	1	40S Ribosomal Protein S16-a
C7	1	40S Ribosomal Protein S17-a
C8	1	40S Ribosomal Protein S18-a
C9	1	40S Ribosomal Protein S19-a
D0	1	40S Ribosomal Protein S20
D1	1	40S Ribosomal Protein S21-a
D2	1	40S Ribosomal Protein S22-a
D3	1	40S Ribosomal Protein S23-a
D4	1	40S Ribosomal Protein S24-a
D5	1	40S Ribosomal Protein S25-a
D6	1	40S Ribosomal Protein S26-b
D7	1	40S Ribosomal Protein S27-a
D8	1	40S Ribosomal Protein S28-a
D9	1	40S Ribosomal Protein S29-a
E0	1	40S Ribosomal Protein S30-a
E1	1	Ubiquitin-40s Ribosomal Protein S31
SR	1	Guanine Nucleotide-binding Protein Subunit Beta-like Protein
SM	1	Suppressor Protein Stm1
Nucleotides(4 molecules)
1	1	25S Ribosomal RNA
3	1	5S Ribosomal RNA
4	1	5.8s Ribosomal RNA
2	1	18S Ribosomal RNA
Chemicals and Non-standard biopolymers (788 molecules)
1	757	MAGNESIUM ION
2	22	(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL
3	9	ZINC ION

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303