GL1X · GenesisL1 explorer

MolNFT v2 · #206379 · protein + RNA

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

8CRE: “Crystal structure of the Candida albicans 80S ribosome in complex with geneticin G418”. X-ray diffraction at 3, 4 ligands (3K5, GET, MG). MolNFT v2 #206379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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
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

Structure

x-ray diffraction · resolution 3 · 112 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
1—rna3216——
3, AT—rna121——
4—rna157——
j, AW—protein249—A0A8H6F1X9
k, AX—protein386—Q59LS1
l, AY—protein361—A0A8H6F4H4
m—protein296—G1UAA6
n—protein157—Q9P834
o, BB—protein234—A0A8H6BVN2
p—protein238—A0A8H6C337
q, BD—protein190—A0A8H6C3N3
r, BE—protein208—Q5AIB8
s, BF—protein171—A0A8H6F1S5
t, BG—protein200—A0A8H6F5V7
u, BH—protein130—A0A8H6F332
v, BI—protein203—Q5A6R1
w, BJ—protein199—A0A8H6BZ56
x—protein173—A0A8H6BUG0
y, BL—protein185—A0A8H6C4Y1
z, BM—protein179—A0A1D8PK40
0, BN—protein170—A0A8H6BZJ3
2, BO—protein159—A0A8H6F1C8
5—protein103—A0A1D8PM41
6, BQ—protein131—A0A8H6C444
7—protein118—A0A8H6C4U1
8—protein121—A0A8H6F6A1
9, BT—protein126—A0A8H6F3X2
AA, BU—protein135—Q9P843
AB, BV—protein148—A0A8H6BVY8
AC—protein62—A0A8H6F0G8
AD, BX—protein96—A0A1D8PM75
AE, BY—protein110—A0A8H6F1M1
AF—protein124—O94008
AG, CA—protein106—A0A8H6BW57
AH, CB—protein112—A0A8H6F171
AI—protein120—A0A8H6F6B7
AJ, CD—protein97—P47834
AK, CE—protein86—A0A1D8PF45
AL, CF—protein77—A0A1D8PG16
AM, CG—protein50—Q96W55
AN—protein52—A0A1D8PL68
AO—protein25—P9WER7
AP, CJ—protein103—A0A8H6BR69
AQ, CK—protein91—A0A1D8PP14
i, CL—protein121—A0A1D8PK71
B—rna1761——
C, CN—protein208—A0A8H6C395
D, CO—protein214—A0A8H6C387
E, CP—protein217—A0A8H6BZ90
F, CQ—protein223—A0A8H6BYS1
G—protein259—A0A1D8PCI6
H, CS—protein206—A0A8H6BS29
I—protein226—A0A8H6BZ37
J—protein185—A0A8H6C655
K, CV—protein203—A0A8H6F0S0
L, CW—protein178—A0A8H6F1X2
M—protein98—A0A8H6BWQ8
N—protein144—A0A1D8PN83
O—protein116—A0A8H6C3A1
P, DA—protein150—A0A8H6F4G0
Q, DB—protein127—A0A8H6F0V4
R—protein129—A0A1D8PK22
S, DD—protein140—O94017
T, DE—protein124—A0A8H6BTR7
U—protein144—A0A8H6F3Y8
V, DG—protein141—A0A8H6C5L4
W—protein102—A0A8H6BYJ9
X, DI—protein87—Q9P844
Y, DJ—protein129—A0A8H6F0N4
Z, DK—protein143—A0A8H6F0V0
a—protein134—A0A8H6C3K1
b—protein72—A0A8H6EZQ8
c, DN—protein98—A0A8H6BTS1
d, DO—protein81—A0A8H6BWE6
e—protein62—A0A8H6C0A5
f—protein55—A0A1D8PTR4
g—protein60—A0A1D8PSK2
h—protein70—Q5A109
AR, DT—protein311—A0A8H6C3E7
AS—rna3229——
AU—rna158——
AZ—protein292—G1UAA6
BA—protein153—Q9P834
BC—protein233—A0A8H6C337
BK—protein176—A0A8H6BUG0
BP—protein102—A0A1D8PM41
BR—protein98—A0A8H6C4U1
BS—protein119—A0A8H6F6A1
BW—protein61—A0A8H6F0G8
BZ—protein124—O94008
CC—protein118—A0A8H6F6B7
CH—protein51—A0A1D8PL68
CI—protein24—P9WER7
CM—rna1765——
CR—protein260—A0A1D8PCI6
CT—protein236—A0A8H6BZ37
CU—protein183—A0A8H6C655
CX—protein94—A0A8H6BWQ8
CY—protein141—A0A1D8PN83
CZ—protein119—A0A8H6C3A1
DC—protein130—A0A1D8PK22
DF—protein141—A0A8H6F3Y8
DH—protein97—A0A8H6BYJ9
DL—protein132—A0A8H6C3K1
DM—protein71—A0A8H6EZQ8
DP—protein61—A0A8H6C0A5
DQ—protein54—A0A1D8PTR4
DR—protein58—A0A1D8PSK2
DS—protein69—Q5A109
P0, p0—protein107—G1UA71
12—protein63—A0A8H6C5X8
L1, l1—protein217—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, j, l, AB, o, AH, k, 4, x, AP, AE, 0, AJ, 8, AN, u, 5, AK, 3, z, v, AG, AF, r, m, n, w, AC, 6, B, AL, t, 9, 2, s, 7, AD, AM, i, Q, P, c, D, G, V, I, H, K, N, g, a, T, J, L, R, E, Y, Z, f, AR, AS, AW, BB, AU, AY, BQ, BV, BW, BO, BJ, BI, BE, CE, CM, CJ, CD, AX, BZ, CG, BT, AZ, AT, CK, BL, BF, BH, BK, BN, CA, CL, DC, DN, DJ, DB, DA, DG, DK, DD, CN, CP, 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.

Compared structures

  • 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

Analyse

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