MolNFT v1 · #172221 · protein + RNA

MBF1-ribosome complex

6ZVI · A/P-site tRNA: “MBF1-ribosome complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.90). MolNFT v1 #172221 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZVI
Type: protein + RNA
Length: 6,864 residues
Chains: 38
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: A/P-site tRNA; P/E-site tRNA; MRNA; 18S rRNA; 40S ribosomal protein S0-a; RPS1A isoform…
UniProt: P32905, A0A6A5PRY4, A0A6A5PWF7, A0A6A5Q3Q1, P0CX35, A0A1L4AA68, P0CX37, P26786, P0CX39, O13516, Q08745, P0CX47, A0A6A5Q8I3, P05756, A0A6A5Q6F2, P0CX51, P02407, P0CX55, P07280, A0A6A5PVE9, P0C0V8, A0A6A5PSE9, P0CX29, P0CX31, A0A6A5PZ18, P35997, A0A6A5Q700, P0CX33, A0A6A5PU37, P38011, A0A6A5Q7X0, A0A6A5PV92, P39516, A0A6A5Q0E8
Ligands: ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 38 distinct chains · 28% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
d	A/P-site tRNA	rna	76	—	—
e	P/E-site tRNA	rna	77	—	—
f	MRNA	rna	35	—	—
h	18S rRNA	rna	1758	—	—
i	40S ribosomal protein S0-a	protein	206	37% helix, 12% strand	P32905
j	RPS1A isoform 1	protein	216	26% helix, 32% strand	A0A6A5PRY4
k	RPS2 isoform 1	protein	217	29% helix, 27% strand	A0A6A5PWF7
l	RPS3 isoform 1	protein	223	34% helix, 28% strand	A0A6A5Q3Q1
m	40S ribosomal protein S4-a	protein	260	15% helix, 30% strand	P0CX35
n	RPS5P	protein	206	44% helix, 4% strand	A0A1L4AA68
o	40S ribosomal protein S6-a	protein	218	26% helix, 25% strand	P0CX37
p	40S ribosomal protein S7-a	protein	185	34% helix, 22% strand	P26786
q	40S ribosomal protein S8-a	protein	188	28% helix, 27% strand	P0CX39
r	40S ribosomal protein S9-a	protein	185	46% helix, 4% strand	O13516
s	40S ribosomal protein S10-a	protein	92	42% helix, 13% strand	Q08745
t	40S ribosomal protein S11-a	protein	146	3% helix, 32% strand	P0CX47
u	RPS12 isoform 1	protein	124	32% helix, 7% strand	A0A6A5Q8I3
v	40S ribosomal protein S13	protein	150	54% helix, 0% strand	P05756
x	RPS15 isoform 1	protein	119	33% helix, 14% strand	A0A6A5Q6F2
y	40S ribosomal protein S16-a	protein	141	34% helix, 21% strand	P0CX51
z	40S ribosomal protein S17-a	protein	125	46% helix, 3% strand	P02407
A	40S ribosomal protein S18-a	protein	145	34% helix, 7% strand	P0CX55
B	40S ribosomal protein S19-a	protein	143	49% helix, 13% strand	P07280
C	RPS20 isoform 1	protein	101	27% helix, 33% strand	A0A6A5PVE9
D	40S ribosomal protein S21-a	protein	87	18% helix, 21% strand	P0C0V8
E	RPS22A isoform 1	protein	129	31% helix, 29% strand	A0A6A5PSE9
H	40S ribosomal protein S23-a	protein	144	23% helix, 24% strand	P0CX29
I	40S ribosomal protein S24-a	protein	134	37% helix, 24% strand	P0CX31
J	RPS25A isoform 1	protein	69	36% helix, 23% strand	A0A6A5PZ18
L	40S ribosomal protein S27-a	protein	81	7% helix, 21% strand	P35997
N	RPS28A isoform 1	protein	63	0% helix, 46% strand	A0A6A5Q700
P	40S ribosomal protein S30-a	protein	46	22% helix, 0% strand	P0CX33
Q	RPS31 isoform 1	protein	73	0% helix, 7% strand	A0A6A5PU37
R	Guanine nucleotide-binding protein subunit beta-like protein	protein	313	1% helix, 51% strand	P38011
T	MBF1 isoform 1	protein	111	40% helix, 0% strand	A0A6A5Q7X0
O	RPS29A isoform 1	protein	53	25% helix, 9% strand	A0A6A5PV92
w	40S ribosomal protein S14-B	protein	128	25% helix, 25% strand	P39516
K	RPS26B isoform 1	protein	97	13% helix, 22% strand	A0A6A5Q0E8

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains L, O

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	1137	0.90	0.92	115	empty
2	762	0.87	0.91	90	empty
3	579	0.87	0.93	67	empty
4	1158	0.87	0.89	121	empty
5	782	0.87	0.90	78	empty

Interfaces

109 interfaces between chains.

h–o · 4961 Å² buried · 111 hydrogen bonds · protein-nucleic
h–q · 4077 Å² buried · 113 hydrogen bonds · protein-nucleic
h–m · 3992 Å² buried · 57 hydrogen bonds · protein-nucleic
h–H · 3862 Å² buried · 78 hydrogen bonds · protein-nucleic
h–r · 3595 Å² buried · 68 hydrogen bonds · protein-nucleic

Compared structures

6ZVI · Mbf1-ribosome complex · the same entry in another collection · chain o against o, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P32905
Every structure of UniProt A0A6A5PRY4
Every structure of UniProt A0A6A5PWF7
Every structure of UniProt A0A6A5Q3Q1
Every structure of UniProt P0CX35
Every structure of UniProt A0A1L4AA68
Every structure of UniProt P0CX37
Every structure of UniProt P26786
Every structure of UniProt P0CX39
Every structure of UniProt O13516
Every structure of UniProt Q08745
Every structure of UniProt P0CX47
Every structure of UniProt A0A6A5Q8I3
Every structure of UniProt P05756
Every structure of UniProt A0A6A5Q6F2
Every structure of UniProt P0CX51
Every structure of UniProt P02407
Every structure of UniProt P0CX55
Every structure of UniProt P07280
Every structure of UniProt A0A6A5PVE9
Every structure of UniProt P0C0V8
Every structure of UniProt A0A6A5PSE9
Every structure of UniProt P0CX29
Every structure of UniProt P0CX31
Every structure of UniProt A0A6A5PZ18
Every structure of UniProt P35997
Every structure of UniProt A0A6A5Q700
Every structure of UniProt P0CX33
Every structure of UniProt A0A6A5PU37
Every structure of UniProt P38011
Every structure of UniProt A0A6A5Q7X0
Every structure of UniProt A0A6A5PV92
Every structure of UniProt P39516
Every structure of UniProt A0A6A5Q0E8
Elsewhere: RCSB PDB 6ZVI · PDBe 6ZVI · UniProt P32905 · UniProt A0A6A5PRY4 · UniProt A0A6A5PWF7 · UniProt A0A6A5Q3Q1 · UniProt P0CX35 · UniProt A0A1L4AA68 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt Q08745 · UniProt P0CX47 · UniProt A0A6A5Q8I3 · UniProt P05756 · UniProt A0A6A5Q6F2 · UniProt P0CX51 · UniProt P02407 · UniProt P0CX55 · UniProt P07280 · UniProt A0A6A5PVE9 · UniProt P0C0V8 · UniProt A0A6A5PSE9 · UniProt P0CX29 · UniProt P0CX31 · UniProt A0A6A5PZ18 · UniProt P35997 · UniProt A0A6A5Q700 · UniProt P0CX33 · UniProt A0A6A5PU37 · UniProt P38011 · UniProt A0A6A5Q7X0 · UniProt A0A6A5PV92 · UniProt P39516 · UniProt A0A6A5Q0E8

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