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Structure of the Candida albicans 80S ribosome in complex with anisomycin

Analyse Structure of the Candida albicans 80S ribosome in complex with anisomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7Q0P
Type: protein + RNA
Length: 16,335 residues
Chains: 80
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.77
Source: Candida albicans SC5314
Molecule: 25S ribosomal RNA; 5S ribosomal RNA; 5.8S ribosomal RNA; Mixture of endogenous E-tRNA…
UniProt: A0A1D8PF08, Q59LS1, A0A1D8PFV1, Q5AGZ7, A0A1D8PCX8, A0A1D8PDL6, Q5ANA1, Q5AEN2, Q5AIB8, A0A1D8PHW1, O59931, A0A1D8PFL9, Q5A6R1, Q5AB87, Q59TE0, A0A1D8PK43, A0A1D8PK40, A0A1D8PLC9, A0A1D8PGY0, A0A1D8PM41, A0A1D8PPT5, Q5A6A1, A0A1D8PPS1, A0A1D8PCQ5, A0A1D8PFG4, A0A1D8PSC5, A0A1D8PF57, A0A1D8PM75, A0A1D8PHF5, A0A1D8PPN6, A0A1D8PHH4, A0A1D8PDZ1, A0A1D8PK30, A0A1D8PH21, A0A1D8PF45, A0A1D8PG16, A0A1D8PDT4, A0A1D8PL68, A0A1D8PEV4, A0A1D8PP14, A0A1D8PK71, O42817, P40910, Q5A900, A0A1D8PSV5, A0A1D8PCI6, Q5AG43, A0A1D8PL99, Q5AJ93, Q59T44, A0A1D8PGY8, A0A1D8PI15, A0A1D8PN83, Q5ADQ6, A0A1D8PPE0, A0A1D8PDT3, A0A1D8PK22, A0A1D8PCW6, A0A1D8PEY9, A0A1D8PQQ5, A0A1D8PK61, Q5A389, A0A1D8PCG7, P0CU35, A0A1D8PDU3, Q5A7K0, A0A1D8PNQ6, Q5ALV6, A0A1D8PTI7, A0A1D8PQN0, A0A1D8PTR4, A0A1D8PSK2, Q5A109, P83774
Ligands: SPD, ANM, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 2.77 · 80 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	25S ribosomal RNA	rna	3209	—	—
3	5S ribosomal RNA	rna	121	—	—
4	5.8S ribosomal RNA	rna	158	—	—
10	Mixture of endogenous E-tRNA	rna	14	—	—
j	Ribosomal 60S subunit protein L2A	protein	249	12% helix, 26% strand	A0A1D8PF08
k	Ribosomal 60S subunit protein L3	protein	386	16% helix, 28% strand	Q59LS1
l	Ribosomal 60S subunit protein L4B	protein	361	32% helix, 10% strand	A0A1D8PFV1
m	Ribosomal 60S subunit protein L5	protein	292	42% helix, 10% strand	Q5AGZ7
n	60S ribosomal protein L6	protein	155	21% helix, 18% strand	A0A1D8PCX8
o	Ribosomal 60S subunit protein L7A	protein	234	55% helix, 15% strand	A0A1D8PDL6
p	60S ribosomal protein L8	protein	238	52% helix, 8% strand	Q5ANA1
q	Ribosomal 60S subunit protein L9B	protein	190	19% helix, 44% strand	Q5AEN2
r	Ribosomal 60S subunit protein L10	protein	208	26% helix, 29% strand	Q5AIB8
s	Ribosomal 60S subunit protein L11B	protein	172	28% helix, 25% strand	A0A1D8PHW1
t	60S ribosomal protein L13	protein	200	45% helix, 9% strand	O59931
u	Ribosomal 60S subunit protein L14B	protein	130	43% helix, 28% strand	A0A1D8PFL9
v	Ribosomal protein L15	protein	203	39% helix, 17% strand	Q5A6R1
w	Ribosomal 60S subunit protein L16A	protein	199	53% helix, 11% strand	Q5AB87
x	Ribosomal 60S subunit protein L17B	protein	172	39% helix, 25% strand	Q59TE0
y	Ribosomal 60S subunit protein L18A	protein	185	31% helix, 15% strand	A0A1D8PK43
z	Ribosomal protein L19	protein	179	69% helix, 3% strand	A0A1D8PK40
0	60S ribosomal protein L20	protein	171	22% helix, 32% strand	A0A1D8PLC9
2	Ribosomal 60S subunit protein L21A	protein	159	19% helix, 25% strand	A0A1D8PGY0
5	Ribosomal 60S subunit protein L22B	protein	103	22% helix, 34% strand	A0A1D8PM41
6	Ribosomal 60S subunit protein L23B	protein	131	8% helix, 36% strand	A0A1D8PPT5
7	Ribosomal 60S subunit protein L24A	protein	63	27% helix, 19% strand	Q5A6A1
8	Ribosomal 60S subunit protein L25	protein	121	26% helix, 21% strand	A0A1D8PPS1
9	Ribosomal 60S subunit protein L26B	protein	126	30% helix, 32% strand	A0A1D8PCQ5
AA	60S ribosomal protein L27	protein	135	26% helix, 27% strand	A0A1D8PFG4
AB	Ribosomal 60S subunit protein L28	protein	148	32% helix, 13% strand	A0A1D8PSC5
AC	60S ribosomal protein L29	protein	63	51% helix, 2% strand	A0A1D8PF57
AD	Ribosomal 60S subunit protein L30	protein	96	43% helix, 18% strand	A0A1D8PM75
AE	Ribosomal 60S subunit protein L31B	protein	109	28% helix, 28% strand	A0A1D8PHF5
AF	Ribosomal 60S subunit protein L32	protein	125	22% helix, 10% strand	A0A1D8PPN6
AG	Ribosomal 60S subunit protein L33A	protein	106	9% helix, 55% strand	A0A1D8PHH4
AH	Ribosomal 60S subunit protein L34B	protein	112	32% helix, 11% strand	A0A1D8PDZ1
AI	Ribosomal 60S subunit protein L35A	protein	119	60% helix, 2% strand	A0A1D8PK30
AJ	60S ribosomal protein L36	protein	98	58% helix, 1% strand	A0A1D8PH21
AK	Ribosomal protein L37	protein	86	19% helix, 7% strand	A0A1D8PF45
AL	Ribosomal 60S subunit protein L38	protein	77	23% helix, 43% strand	A0A1D8PG16
AM	60S ribosomal protein L39	protein	50	30% helix, 0% strand	A0A1D8PDT4
AN	Rpl40bp	protein	52	21% helix, 15% strand	A0A1D8PL68
AO	60S ribosomal protein L41	protein	24	88% helix, 0% strand	—
AP	Ribosomal 60S subunit protein L42A	protein	103	10% helix, 36% strand	A0A1D8PEV4
AQ	Ribosomal 60S subunit protein L43A	protein	91	42% helix, 12% strand	A0A1D8PP14
i	HABP4_PAI-RBP1 domain-containing protein	protein	113	31% helix, 1% strand	A0A1D8PK71
A	18S ribosomal RNA	rna	1692	—	—
B	40S ribosomal protein S0	protein	208	37% helix, 15% strand	O42817
C	40S ribosomal protein S1	protein	214	31% helix, 36% strand	P40910
D	Ribosomal 40S subunit protein S2	protein	216	31% helix, 27% strand	Q5A900
E	Ribosomal 40S subunit protein S3	protein	223	33% helix, 29% strand	A0A1D8PSV5
F	40S ribosomal protein S4	protein	260	18% helix, 32% strand	A0A1D8PCI6
G	Ribosomal 40S subunit protein S5	protein	206	47% helix, 7% strand	Q5AG43
H	40S ribosomal protein S6	protein	226	26% helix, 27% strand	A0A1D8PL99
I	40S ribosomal protein S7	protein	182	33% helix, 23% strand	Q5AJ93
J	40S ribosomal protein S8	protein	203	33% helix, 26% strand	Q59T44
K	Ribosomal 40S subunit protein S9B	protein	178	49% helix, 6% strand	A0A1D8PGY8
L	Ribosomal 40S subunit protein S10A	protein	93	33% helix, 19% strand	A0A1D8PI15
M	Ribosomal 40S subunit protein S11A	protein	141	3% helix, 35% strand	A0A1D8PN83
N	40S ribosomal protein S12	protein	116	28% helix, 7% strand	Q5ADQ6
O	Ribosomal 40S subunit protein S13	protein	150	55% helix, 0% strand	A0A1D8PPE0
P	Ribosomal 40S subunit protein S14B	protein	127	27% helix, 27% strand	A0A1D8PDT3
Q	Ribosomal 40S subunit protein S15	protein	118	39% helix, 16% strand	A0A1D8PK22
R	Ribosomal 40S subunit protein S16A	protein	140	42% helix, 20% strand	A0A1D8PCW6
S	Ribosomal 40S subunit protein S17B	protein	125	46% helix, 3% strand	A0A1D8PEY9
T	Ribosomal 40S subunit protein S18B	protein	142	42% helix, 8% strand	A0A1D8PQQ5
U	Ribosomal 40S subunit protein S19A	protein	141	46% helix, 11% strand	A0A1D8PK61
V	Ribosomal 40S subunit protein S20	protein	100	27% helix, 43% strand	Q5A389
W	40S ribosomal protein S21	protein	87	18% helix, 24% strand	A0A1D8PCG7
X	40S ribosomal protein S22-B	protein	129	33% helix, 26% strand	P0CU35
Y	Ribosomal 40S subunit protein S23B	protein	143	24% helix, 29% strand	A0A1D8PDU3
Z	40S ribosomal protein S24	protein	132	39% helix, 27% strand	Q5A7K0
a	40S ribosomal protein S25	protein	72	47% helix, 17% strand	A0A1D8PNQ6
b	40S ribosomal protein S26	protein	100	15% helix, 23% strand	Q5ALV6
c	40S ribosomal protein S27	protein	81	7% helix, 23% strand	A0A1D8PTI7
d	Ribosomal 40S subunit protein S28B	protein	62	0% helix, 44% strand	A0A1D8PQN0
e	Ribosomal 40S subunit protein S29A	protein	55	22% helix, 11% strand	A0A1D8PTR4
f	40S ribosomal protein S30	protein	56	30% helix, 0% strand	A0A1D8PSK2
g	Ubiquitin-ribosomal 40S subunit protein S31 fusion protein	protein	70	7% helix, 13% strand	Q5A109
h	Guanine nucleotide-binding protein subunit beta-like protein	protein	311	0% helix, 51% strand	P83774

Ligands and binding sites

SPD · Spermidine · ligand · 2 copies · chains 1, AB, AP
ANM · Anisomycin · ligand · chains 1
ZN · Zinc ion · metal · 8 copies · chains AK, AN, AP, AQ, A, P, b, c, e, g

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	971	0.89	0.91	102	empty
2	931	0.89	0.91	96	empty
3	1127	0.88	0.90	102	empty
4	1133	0.88	0.90	118	empty
5	558	0.88	0.94	67	SPD

Interfaces

243 interfaces between chains.

1–k · 9184 Å² buried · 222 hydrogen bonds · protein-nucleic
1–l · 8583 Å² buried · 182 hydrogen bonds · protein-nucleic
1–v · 7450 Å² buried · 162 hydrogen bonds · protein-nucleic
1–j · 7158 Å² buried · 191 hydrogen bonds · protein-nucleic
1–z · 5232 Å² buried · 127 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 6 modified, 1 covalent, 1 disulfide (methylation, nucleotide modification, covalent ligand, disulfide, nonstandard).

Compared structures

O42817 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S0 (O42817) · a predicted model of the same protein · chain B against A, TM-score 0.99
P40910 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S1 (P40910) · a predicted model of the same protein · chain C against A, TM-score 0.99
P0CU35 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S22-B (P0CU35) · a predicted model of the same protein · chain X against A, TM-score 0.99
P83774 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein subunit… · a predicted model of the same protein · chain h against A, TM-score 0.98
O59931 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L13 (O59931) · a predicted model of the same protein · chain t against A, TM-score 0.96

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