Research workbench

EDF1-ribosome complex

Analyse EDF1-ribosome complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZVH
Type: protein + RNA
Length: 6,889 residues
Chains: 37
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S rRNA; 40S ribosomal protein sa; 40S ribosomal protein S3A; 40S ribosomal protein S3…
EC: 4.2.99.18
UniProt: P08865, P61247, P23396, P62701, P46782, P62081, P62241, P46783, P62280, P62841, P62249, P08708, P62269, P39019, P60866, P63220, P62266, P62854, P62857, P62273, P63244, P15880, P62753, P46781, P25398, P62277, P62263, P62244, P62847, P62851, P42677, P62861, P62979, Q9NX58, O60869
Ligands: MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 37 distinct chains · 30% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S rRNA	rna	1740	—	—
A	40S ribosomal protein sa	protein	221	39% helix, 12% strand	P08865
B	40S ribosomal protein S3A	protein	214	29% helix, 30% strand	P61247
D	40S ribosomal protein S3 (EC 4.2.99.18)	protein	227	31% helix, 22% strand	P23396
E	40S ribosomal protein S4, X isoform	protein	262	17% helix, 28% strand	P62701
F	40S ribosomal protein S5	protein	184	51% helix, 5% strand	P46782
H	40S ribosomal protein S7	protein	186	30% helix, 19% strand	P62081
I	40S ribosomal protein S8	protein	206	29% helix, 25% strand	P62241
K	40S ribosomal protein S10	protein	98	37% helix, 14% strand	P46783
L	40S ribosomal protein S11	protein	153	3% helix, 29% strand	P62280
P	40S ribosomal protein S15	protein	129	35% helix, 12% strand	P62841
Q	40S ribosomal protein S16	protein	144	34% helix, 20% strand	P62249
R	40S ribosomal protein S17	protein	135	50% helix, 4% strand	P08708
S	40S ribosomal protein S18	protein	145	39% helix, 7% strand	P62269
T	40S ribosomal protein S19	protein	143	48% helix, 13% strand	P39019
U	40S ribosomal protein S20	protein	104	24% helix, 38% strand	P60866
V	40S ribosomal protein S21	protein	83	18% helix, 24% strand	P63220
X	40S ribosomal protein S23	protein	141	23% helix, 26% strand	P62266
a	40S ribosomal protein S26	protein	102	20% helix, 20% strand	P62854
c	40S ribosomal protein S28	protein	64	0% helix, 33% strand	P62857
d	40S ribosomal protein S29	protein	55	25% helix, 11% strand	P62273
g	Receptor of activated protein C kinase 1	protein	313	0% helix, 46% strand	P63244
C	40S ribosomal protein S2	protein	222	34% helix, 27% strand	P15880
G	40S ribosomal protein S6	protein	237	28% helix, 24% strand	P62753
J	40S ribosomal protein S9	protein	185	52% helix, 5% strand	P46781
M	40S ribosomal protein S12	protein	122	45% helix, 11% strand	P25398
N	40S ribosomal protein S13	protein	150	55% helix, 0% strand	P62277
O	40S ribosomal protein S14	protein	140	21% helix, 24% strand	P62263
W	40S ribosomal protein S15A	protein	129	33% helix, 29% strand	P62244
Y	40S ribosomal protein S24	protein	131	32% helix, 29% strand	P62847
Z	40S ribosomal protein S25	protein	75	40% helix, 9% strand	P62851
b	40S ribosomal protein S27	protein	83	7% helix, 24% strand	P42677
e	40S ribosomal protein S30	protein	42	38% helix, 2% strand	P62861
f	Ubiquitin-40S ribosomal protein S27A	protein	67	0% helix, 15% strand	P62979
x	E-site tRNA	rna	75	—	—
y	Cell growth-regulating nucleolar protein	protein	72	57% helix, 14% strand	Q9NX58
i	Endothelial differentiation-related factor 1	protein	110	47% helix, 1% strand	O60869

Ligands and binding sites

MG · Magnesium ion · metal · 30 copies · chains 2, a, I, Q, O, G
ZN · Zinc ion · metal · 3 copies · chains a, d, f

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	1130	0.89	0.91	91	MG
2	1155	0.88	0.90	104	empty
3	790	0.86	0.89	78	empty
4	823	0.86	0.89	87	empty
5	799	0.86	0.89	74	empty

Interfaces

99 interfaces between chains.

2–G · 5540 Å² buried · 116 hydrogen bonds · protein-nucleic
2–I · 4197 Å² buried · 90 hydrogen bonds · protein-nucleic
2–E · 3808 Å² buried · 63 hydrogen bonds · protein-nucleic
2–J · 3567 Å² buried · 78 hydrogen bonds · protein-nucleic
2–X · 3429 Å² buried · 73 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6ZVH · EDF1-ribosome complex · the same entry in another collection · chain P against P, 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 P08865
Every structure of UniProt P61247
Every structure of UniProt P23396
Every structure of UniProt P62701
Every structure of UniProt P46782
Every structure of UniProt P62081
Every structure of UniProt P62241
Every structure of UniProt P46783
Every structure of UniProt P62280
Every structure of UniProt P62841
Every structure of UniProt P62249
Every structure of UniProt P08708
Every structure of UniProt P62269
Every structure of UniProt P39019
Every structure of UniProt P60866
Every structure of UniProt P63220
Every structure of UniProt P62266
Every structure of UniProt P62854
Every structure of UniProt P62857
Every structure of UniProt P62273
Every structure of UniProt P63244
Every structure of UniProt P15880
Every structure of UniProt P62753
Every structure of UniProt P46781
Every structure of UniProt P25398
Every structure of UniProt P62277
Every structure of UniProt P62263
Every structure of UniProt P62244
Every structure of UniProt P62847
Every structure of UniProt P62851
Every structure of UniProt P42677
Every structure of UniProt P62861
Every structure of UniProt P62979
Every structure of UniProt Q9NX58
Every structure of UniProt O60869
Elsewhere: RCSB PDB 6ZVH · PDBe 6ZVH · UniProt P08865 · UniProt P61247 · UniProt P23396 · UniProt P62701 · UniProt P46782 · UniProt P62081 · UniProt P62241 · UniProt P46783 · UniProt P62280 · UniProt P62841 · UniProt P62249 · UniProt P08708 · UniProt P62269 · UniProt P39019 · UniProt P60866 · UniProt P63220 · UniProt P62266 · UniProt P62854 · UniProt P62857 · UniProt P62273 · UniProt P63244 · UniProt P15880 · UniProt P62753 · UniProt P46781 · UniProt P25398 · UniProt P62277 · UniProt P62263 · UniProt P62244 · UniProt P62847 · UniProt P62851 · UniProt P42677 · UniProt P62861 · UniProt P62979 · UniProt Q9NX58 · UniProt O60869

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