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8P9A: 80S yeast ribosome in complex with Methyllissoclimide

PDB ID:	8P9A Download
MMDB ID:	255630
PDB Deposition Date:	2023/6/5
Updated in MMDB:	2024/12
Experimental Method:	x-ray diffraction
Resolution:	2.9 Å
Source Organism:	Saccharomyces cerevisiae
Similar Structures:

Biological Unit for 8P9A: 158-meric; determined by author

Molecular Components in 8P9A
Label	Count	Molecule
Proteins (150 molecules)
j CD	2	60S Ribosomal Protein L2-a
k CE	2	60S Ribosomal Protein L3
l CF	2	60S Ribosomal Protein L4-a
m CG	2	60S Ribosomal Protein L5
n CH	2	60S Ribosomal Protein L6-a
o CI	2	60S Ribosomal Protein L7-a
p CJ	2	60S Ribosomal Protein L8-a
q CK	2	60S Ribosomal Protein L9-a
r CL	2	60S Ribosomal Protein L10
s CM	2	Large Ribosomal Subunit Protein Ul5b
t CN	2	60S Ribosomal Protein L13-a
u CO	2	60S Ribosomal Protein L14-a
v CP	2	60S Ribosomal Protein L15-a
w CQ	2	60S Ribosomal Protein L16-a
x CR	2	60S Ribosomal Protein L17-a
y CS	2	60S Ribosomal Protein L18-a
z CT	2	60S Ribosomal Protein L19-a
0 CU	2	60S Ribosomal Protein L20-a
2 CV	2	60S Ribosomal Protein L21-a
5 CW	2	60S Ribosomal Protein L22-a
6 CX	2	60S Ribosomal Protein L23-a
7 CY	2	60S Ribosomal Protein L24-a
8 CZ	2	60S Ribosomal Protein L25
9 DA	2	60S Ribosomal Protein L26-a
AA DB	2	60S Ribosomal Protein L27-a
AB DC	2	60S Ribosomal Protein L28
AC DD	2	60S Ribosomal Protein L29
AD DE	2	60S Ribosomal Protein L30
AE DF	2	60S Ribosomal Protein L31-a
AF DG	2	60S Ribosomal Protein L32
AG DH	2	60S Ribosomal Protein L33-a
AH DI	2	60S Ribosomal Protein L34-a
AI DJ	2	60S Ribosomal Protein L35-a
AJ DK	2	60S Ribosomal Protein L36-a
AK DL	2	60S Ribosomal Protein L37-a
AL DM	2	60S Ribosomal Protein L38
AM DN	2	60S Ribosomal Protein L39
AN DO	2	Ubiquitin-60s Ribosomal Protein L40
AO DP	2	Large Ribosomal Subunit Protein El41b
AP DQ	2	60S Ribosomal Protein L42-a
AQ DR	2	60S Ribosomal Protein L43-a
i sM	2	Suppressor Protein Stm1
p0	1	60S Acidic Ribosomal Protein P0
B s0	2	40S Ribosomal Protein S0-a
C s1	2	40S Ribosomal Protein S1-a
D s2	2	40S Ribosomal Protein S2
E s3	2	Small Ribosomal Subunit Protein US3
F s4	2	40S Ribosomal Protein S4-a
G s5	2	40S Ribosomal Protein S5
H s6	2	40S Ribosomal Protein S6-a
I s7	2	40S Ribosomal Protein S7-a
J s8	2	40S Ribosomal Protein S8-a
K s9	2	40S Ribosomal Protein S9-a
L c0	2	40S Ribosomal Protein S10-a
M c1	2	40S Ribosomal Protein S11-a
N	1	40S Ribosomal Protein S12
O c3	2	40S Ribosomal Protein S13
P c4	2	40S Ribosomal Protein S14-b
Q c5	2	40S Ribosomal Protein S15
R c6	2	40S Ribosomal Protein S16-a
S c7	2	40S Ribosomal Protein S17-a
T c8	2	40S Ribosomal Protein S18-a
U c9	2	40S Ribosomal Protein S19-a
V d0	2	Small Ribosomal Subunit Protein Us10
W d1	2	40S Ribosomal Protein S21-a
X d2	2	40S Ribosomal Protein S22-a
Y d3	2	40S Ribosomal Protein S23-a
Z d4	2	40S Ribosomal Protein S24-a
a d5	2	40S Ribosomal Protein S25-a
b d6	2	Small Ribosomal Subunit Protein Es26b
c d7	2	40S Ribosomal Protein S27-a
d d8	2	40S Ribosomal Protein S28-a
e d9	2	Small Ribosomal Subunit Protein Us14a
f e0	2	40S Ribosomal Protein S30-a
g e1	2	Ubiquitin
h Rb	2	Guanine Nucleotide-binding Protein Subunit Beta-like Protein
Nucleotides(8 molecules)
1 AR	2	25S Ribosomal RNA
3 AS	2	5S Ribosomal RNA
4 AT	2	5.8 Ribosomal RNA
A sR	2	16S Ribosomal RNA
Chemicals and Non-standard biopolymers (2417 molecules)
1	930	osmium (III) hexammine
2	1465	MAGNESIUM ION
3	2	SPERMIDINE
4	2	(3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione
5	18	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