Research workbench

Crystal structure of the Candida albicans 80S ribosome in complex with geneticin G418

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

PDB: 8CRE
Type: protein + RNA
Length: 33,667 residues
Chains: 163
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3
Source: Candida albicans
Molecule: 25S; 5S; 5.8S; 60S ribosomal protein L2-B; 60S ribosomal protein L3; 60S ribosomal…
UniProt: A0A8H6F1X9, Q59LS1, A0A8H6F4H4, G1UAA6, Q9P834, A0A8H6BVN2, A0A8H6C337, A0A8H6C3N3, Q5AIB8, A0A8H6F1S5, A0A8H6F5V7, A0A8H6F332, Q5A6R1, A0A8H6BZ56, A0A8H6BUG0, A0A8H6C4Y1, A0A1D8PK40, A0A8H6BZJ3, A0A8H6F1C8, A0A1D8PM41, A0A8H6C444, A0A8H6C4U1, A0A8H6F6A1, A0A8H6F3X2, Q9P843, A0A8H6BVY8, A0A8H6F0G8, A0A1D8PM75, A0A8H6F1M1, O94008, A0A8H6BW57, A0A8H6F171, A0A8H6F6B7, P47834, A0A1D8PF45, A0A1D8PG16, Q96W55, A0A1D8PL68, P9WER7, A0A8H6BR69, A0A1D8PP14, A0A1D8PK71, A0A8H6C395, A0A8H6C387, A0A8H6BZ90, A0A8H6BYS1, A0A1D8PCI6, A0A8H6BS29, A0A8H6BZ37, A0A8H6C655, A0A8H6F0S0, A0A8H6F1X2, A0A8H6BWQ8, A0A1D8PN83, A0A8H6C3A1, A0A8H6F4G0, A0A8H6F0V4, A0A1D8PK22, O94017, A0A8H6BTR7, A0A8H6F3Y8, A0A8H6C5L4, A0A8H6BYJ9, Q9P844, A0A8H6F0N4, A0A8H6F0V0, A0A8H6C3K1, A0A8H6EZQ8, A0A8H6BTS1, A0A8H6BWE6, A0A8H6C0A5, A0A1D8PTR4, A0A1D8PSK2, Q5A109, A0A8H6C3E7, G1UA71, A0A8H6C5X8, A0A8H6F4E7
Ligands: 3K5, GET, MG, ZN
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · resolution 3 · 112 distinct chains · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	25S	rna	3216	—	—
3, AT	5S	rna	121	—	—
4	5.8S	rna	157	—	—
j, AW	60S ribosomal protein L2-B	protein	249	12% helix, 25% strand	A0A8H6F1X9
k, AX	60S ribosomal protein L3	protein	386	17% helix, 28% strand	Q59LS1
l, AY	60S ribosomal protein L4-B	protein	361	32% helix, 9% strand	A0A8H6F4H4
m	Uncharacterized protein CaJ7.0206	protein	296	46% helix, 10% strand	G1UAA6
n	60S ribosomal protein L6	protein	157	22% helix, 20% strand	Q9P834
o, BB	60S ribosomal protein L7-A	protein	234	56% helix, 16% strand	A0A8H6BVN2
p	60S ribosomal protein L8	protein	238	50% helix, 8% strand	A0A8H6C337
q, BD	60S ribosomal protein L9-B	protein	190	19% helix, 44% strand	A0A8H6C3N3
r, BE	60S ribosomal protein L10	protein	208	25% helix, 25% strand	Q5AIB8
s, BF	60S ribosomal protein L11-B	protein	171	29% helix, 25% strand	A0A8H6F1S5
t, BG	60S ribosomal protein L13	protein	200	45% helix, 9% strand	A0A8H6F5V7
u, BH	60S ribosomal protein L14-B	protein	130	43% helix, 28% strand	A0A8H6F332
v, BI	60S ribosomal protein L15-A	protein	203	39% helix, 17% strand	Q5A6R1
w, BJ	Ribosomal protein L13	protein	199	56% helix, 11% strand	A0A8H6BZ56
x	Ribosomal protein L22	protein	173	39% helix, 25% strand	A0A8H6BUG0
y, BL	60S ribosomal protein L18-A	protein	185	32% helix, 15% strand	A0A8H6C4Y1
z, BM	60S ribosomal protein L19-A	protein	179	69% helix, 3% strand	A0A1D8PK40
0, BN	60S ribosomal protein L20	protein	170	22% helix, 32% strand	A0A8H6BZJ3
2, BO	60S ribosomal protein L21-A	protein	159	18% helix, 25% strand	A0A8H6F1C8
5	60S ribosomal protein L22-B	protein	103	24% helix, 34% strand	A0A1D8PM41
6, BQ	60S ribosomal protein L23-A	protein	131	11% helix, 36% strand	A0A8H6C444
7	60S ribosomal protein L24-A	protein	118	49% helix, 12% strand	A0A8H6C4U1
8	60S ribosomal protein L25	protein	121	26% helix, 21% strand	A0A8H6F6A1
9, BT	Ribosomal protein L24	protein	126	30% helix, 32% strand	A0A8H6F3X2
AA, BU	60S ribosomal protein L27	protein	135	26% helix, 27% strand	Q9P843
AB, BV	60S ribosomal protein L28	protein	148	29% helix, 13% strand	A0A8H6BVY8
AC	60S ribosomal protein L29	protein	62	52% helix, 2% strand	A0A8H6F0G8
AD, BX	60S ribosomal protein L30	protein	96	43% helix, 18% strand	A0A1D8PM75
AE, BY	60S ribosomal protein L31-B	protein	110	31% helix, 26% strand	A0A8H6F1M1
AF	60S ribosomal protein L32	protein	124	22% helix, 10% strand	O94008
AG, CA	60S ribosomal protein L33-A	protein	106	9% helix, 55% strand	A0A8H6BW57
AH, CB	60S ribosomal protein L34-B	protein	112	32% helix, 11% strand	A0A8H6F171
AI	Ribosomal protein L29	protein	120	61% helix, 2% strand	A0A8H6F6B7
AJ, CD	60S ribosomal protein L36	protein	97	59% helix, 1% strand	P47834
AK, CE	60S ribosomal protein L37-B	protein	86	19% helix, 7% strand	A0A1D8PF45
AL, CF	60S ribosomal protein L38	protein	77	23% helix, 43% strand	A0A1D8PG16
AM, CG	60S ribosomal protein L39	protein	50	34% helix, 0% strand	Q96W55
AN	60S ribosomal protein L40-B	protein	52	21% helix, 15% strand	A0A1D8PL68
AO	60S ribosomal protein L41	protein	25	88% helix, 0% strand	P9WER7
AP, CJ	60S ribosomal protein L42-B	protein	103	10% helix, 34% strand	A0A8H6BR69
AQ, CK	60S ribosomal protein L43-A	protein	91	42% helix, 12% strand	A0A1D8PP14
i, CL	60S ribosomal protein CAALFM_C304810CA	protein	121	27% helix, 2% strand	A0A1D8PK71
B	18S	rna	1761	—	—
C, CN	40S ribosomal protein S0	protein	208	37% helix, 15% strand	A0A8H6C395
D, CO	40S ribosomal protein S1	protein	214	29% helix, 36% strand	A0A8H6C387
E, CP	Ribosomal protein S5	protein	217	31% helix, 27% strand	A0A8H6BZ90
F, CQ	Ribosomal protein S3	protein	223	34% helix, 28% strand	A0A8H6BYS1
G	40S ribosomal protein S4	protein	259	18% helix, 30% strand	A0A1D8PCI6
H, CS	Ribosomal protein S7	protein	206	45% helix, 7% strand	A0A8H6BS29
I	40S ribosomal protein S6	protein	226	26% helix, 28% strand	A0A8H6BZ37
J	40S ribosomal protein S7	protein	185	32% helix, 23% strand	A0A8H6C655
K, CV	40S ribosomal protein S8	protein	203	33% helix, 26% strand	A0A8H6F0S0
L, CW	Ribosomal protein S4	protein	178	49% helix, 6% strand	A0A8H6F1X2
M	40S ribosomal protein S10-A	protein	98	32% helix, 16% strand	A0A8H6BWQ8
N	40S ribosomal protein S11A	protein	144	3% helix, 36% strand	A0A1D8PN83
O	40S ribosomal protein S12	protein	116	33% helix, 6% strand	A0A8H6C3A1
P, DA	40S ribosomal protein S13	protein	150	56% helix, 0% strand	A0A8H6F4G0
Q, DB	40S ribosomal protein S14-A	protein	127	28% helix, 28% strand	A0A8H6F0V4
R	40S ribosomal protein S15	protein	129	36% helix, 16% strand	A0A1D8PK22
S, DD	40S ribosomal protein S16	protein	140	44% helix, 20% strand	O94017
T, DE	40S ribosomal protein S17-B	protein	124	47% helix, 3% strand	A0A8H6BTR7
U	40S ribosomal protein S18-B	protein	144	44% helix, 8% strand	A0A8H6F3Y8
V, DG	40S ribosomal protein S19-A	protein	141	47% helix, 11% strand	A0A8H6C5L4
W	Ribosomal protein S10	protein	102	26% helix, 46% strand	A0A8H6BYJ9
X, DI	40S ribosomal protein S21	protein	87	18% helix, 24% strand	Q9P844
Y, DJ	40S ribosomal protein S22-A	protein	129	34% helix, 26% strand	A0A8H6F0N4
Z, DK	Ribosomal protein S23 (S12)	protein	143	24% helix, 27% strand	A0A8H6F0V0
a	40S ribosomal protein S24	protein	134	37% helix, 27% strand	A0A8H6C3K1
b	40S ribosomal protein S25	protein	72	47% helix, 18% strand	A0A8H6EZQ8
c, DN	40S ribosomal protein S26	protein	98	16% helix, 24% strand	A0A8H6BTS1
d, DO	40S ribosomal protein S27	protein	81	7% helix, 22% strand	A0A8H6BWE6
e	40S ribosomal protein S28-B	protein	62	0% helix, 47% strand	A0A8H6C0A5
f	40S ribosomal protein S29A	protein	55	25% helix, 11% strand	A0A1D8PTR4
g	40S ribosomal protein S30	protein	60	28% helix, 0% strand	A0A1D8PSK2
h	Ubiquitin-40S ribosomal protein S31 fusion protein	protein	70	7% helix, 11% strand	Q5A109
AR, DT	Guanine nucleotide-binding protein subunit beta-like protein	protein	311	0% helix, 51% strand	A0A8H6C3E7
AS	25S	rna	3229	—	—
AU	5.8S	rna	158	—	—
AZ	Uncharacterized protein CaJ7.0206	protein	292	42% helix, 10% strand	G1UAA6
BA	60S ribosomal protein L6	protein	153	22% helix, 18% strand	Q9P834
BC	60S ribosomal protein L8	protein	233	51% helix, 8% strand	A0A8H6C337
BK	Ribosomal protein L22	protein	176	38% helix, 26% strand	A0A8H6BUG0
BP	60S ribosomal protein L22-B	protein	102	27% helix, 31% strand	A0A1D8PM41
BR	60S ribosomal protein L24-A	protein	98	37% helix, 13% strand	A0A8H6C4U1
BS	60S ribosomal protein L25	protein	119	27% helix, 21% strand	A0A8H6F6A1
BW	60S ribosomal protein L29	protein	61	52% helix, 2% strand	A0A8H6F0G8
BZ	60S ribosomal protein L32	protein	124	22% helix, 10% strand	O94008
CC	Ribosomal protein L29	protein	118	62% helix, 2% strand	A0A8H6F6B7
CH	60S ribosomal protein L40-B	protein	51	18% helix, 16% strand	A0A1D8PL68
CI	60S ribosomal protein L41	protein	24	79% helix, 0% strand	P9WER7
CM	18S	rna	1765	—	—
CR	40S ribosomal protein S4	protein	260	18% helix, 30% strand	A0A1D8PCI6
CT	40S ribosomal protein S6	protein	236	29% helix, 27% strand	A0A8H6BZ37
CU	40S ribosomal protein S7	protein	183	31% helix, 23% strand	A0A8H6C655
CX	40S ribosomal protein S10-A	protein	94	40% helix, 19% strand	A0A8H6BWQ8
CY	40S ribosomal protein S11A	protein	141	3% helix, 33% strand	A0A1D8PN83
CZ	40S ribosomal protein S12	protein	119	29% helix, 4% strand	A0A8H6C3A1
DC	40S ribosomal protein S15	protein	130	35% helix, 15% strand	A0A1D8PK22
DF	40S ribosomal protein S18-B	protein	141	40% helix, 7% strand	A0A8H6F3Y8
DH	Ribosomal protein S10	protein	97	28% helix, 41% strand	A0A8H6BYJ9
DL	40S ribosomal protein S24	protein	132	39% helix, 27% strand	A0A8H6C3K1
DM	40S ribosomal protein S25	protein	71	46% helix, 17% strand	A0A8H6EZQ8
DP	40S ribosomal protein S28-B	protein	61	0% helix, 49% strand	A0A8H6C0A5
DQ	40S ribosomal protein S29A	protein	54	26% helix, 11% strand	A0A1D8PTR4
DR	40S ribosomal protein S30	protein	58	29% helix, 0% strand	A0A1D8PSK2
DS	Ubiquitin-40S ribosomal protein S31 fusion protein	protein	69	7% helix, 14% strand	Q5A109
P0, p0	60S acidic ribosomal protein P0	protein	107	46% helix, 6% strand	G1UA71
12	60S ribosomal protein L12-A	protein	63	40% helix, 3% strand	A0A8H6C5X8
L1, l1	Ribosomal protein	protein	217	34% helix, 10% strand	A0A8H6F4E7

Ligands and binding sites

3K5 · 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose · ligand · 2 copies · chains 1, AP, AS, CJ
GET · Geneticin · ligand · 2 copies · chains B, g, CM
MG · Magnesium ion · metal · 1210 copies · chains 1, v, j, l, k, 7, AB, o, AM, AH, q, AE, z, AK, 4, AQ, 2, x, y, AP, 0, 8, AJ, 6, AN, AO, B, AC, u, 5, 3, w, AG, AF, r, m, n, t, AL, 9, s, AD, i, Q, P, G, c, D, F, N, V, S, W, I, Y, R, H, K, g, a, T, J, L, E, Z, f, AR, AS, BV, AW, BB, BI, AX, AU, AY, BQ, BZ, BD, CE, BW, BO, BJ, BE, CM, CJ, CD, CG, BS, BT, AZ, AT, CK, BL, BF, BH, BK, BN, CA, CL, DC, DF, DN, CP, DJ, DB, DA, DG, DD, DK, CY, CR, CN, DI, CQ, DQ
ZN · Zinc ion · metal · 18 copies · chains AH, AK, AN, AP, AQ, c, d, f, h, CB, CE, CH, CJ, CK, DN, DO, DQ, DS

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	1002	0.90	0.93	89	MG
2	1596	0.90	0.92	137	MG
3	1887	0.90	0.92	132	MG
4	906	0.90	0.93	86	MG
5	926	0.89	0.92	90	empty

Interfaces

511 interfaces between chains.

1–k · 9283 Å² buried · 241 hydrogen bonds · protein-nucleic
AS–AX · 9210 Å² buried · 235 hydrogen bonds · protein-nucleic
AS–AY · 8703 Å² buried · 189 hydrogen bonds · protein-nucleic
1–l · 8641 Å² buried · 189 hydrogen bonds · protein-nucleic
AS–BI · 7638 Å² buried · 179 hydrogen bonds · protein-nucleic

Compared structures

Q9P843 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L27 (Q9P843) · a predicted model of the same protein · chain AA against A, TM-score 0.99
O94017 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S16 (O94017) · a predicted model of the same protein · chain S against A, TM-score 0.99
Q9P844 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S21 (Q9P844) · a predicted model of the same protein · chain X against A, TM-score 0.98
O94008 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L32 (O94008) · a predicted model of the same protein · chain BZ against A, TM-score 0.98
P47834 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L36 (P47834) · a predicted model of the same protein · chain AJ against A, TM-score 0.96
Q96W55 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L39 (Q96W55) · a predicted model of the same protein · chain AM against A, TM-score 0.95

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.