Research workbench

Structure of a human 48S translational initiation complex - EIF3

Analyse Structure of a human 48S translational initiation complex - EIF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YBD
Type: protein
Length: 4,421 residues
Chains: 19
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic translation initiation factor 3 subunit M; Eukaryotic translation initiation…
EC: 3.4.19.12
UniProt: Q7L2H7, O00303, Q14152, P60228, Q99613, O15372, P62081, P42677, P63220, P08708, P15880, P61247, P08865, P62854, P62263, P62277, O15371, Q9UBQ5, Q9Y262
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 19 distinct chains · 42% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
6	Eukaryotic translation initiation factor 3 subunit M	protein	350	37% helix, 0% strand	Q7L2H7
4	Eukaryotic translation initiation factor 3 subunit F (EC 3.4.19.12)	protein	257	45% helix, 11% strand	O00303
u	Eukaryotic translation initiation factor 3 subunit a	protein	572	59% helix, 2% strand	Q14152
v	Eukaryotic translation initiation factor 3 subunit E	protein	384	45% helix, 2% strand	P60228
y	Eukaryotic translation initiation factor 3 subunit C	protein	535	57% helix, 3% strand	Q99613
8	Eukaryotic translation initiation factor 3 subunit H	protein	317	42% helix, 12% strand	O15372
G	40S ribosomal protein S7	protein	177	24% helix, 18% strand	P62081
H	40S ribosomal protein S27	protein	81	4% helix, 22% strand	P42677
K	40S ribosomal protein S21	protein	81	19% helix, 10% strand	P63220
M	40S ribosomal protein S17	protein	54	17% helix, 11% strand	P08708
L	40S ribosomal protein S2	protein	220	26% helix, 22% strand	P15880
O	40S ribosomal protein S3A	protein	211	22% helix, 30% strand	P61247
N	40S ribosomal protein sa	protein	207	30% helix, 14% strand	P08865
Q	40S ribosomal protein S26	protein	99	8% helix, 24% strand	P62854
P	40S ribosomal protein S14	protein	133	21% helix, 25% strand	P62263
I	40S ribosomal protein S13	protein	150	34% helix, 0% strand	P62277
x	Eukaryotic translation initiation factor 3 subunit D	protein	61	0% helix, 2% strand	O15371
3	Eukaryotic translation initiation factor 3 subunit K	protein	213	65% helix, 2% strand	Q9UBQ5
5	Eukaryotic translation initiation factor 3 subunit L	protein	319	68% helix, 3% strand	Q9Y262

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	936	0.85	0.87	162	empty
2	1067	0.85	0.85	88	empty
3	1060	0.83	0.84	156	empty
4	1116	0.77	0.79	79	empty
5	1167	0.77	0.79	124	empty

Interfaces

37 interfaces between chains.

u–y · 2767 Å² buried · 30 hydrogen bonds · protein-protein
y–x · 2101 Å² buried · 16 hydrogen bonds · protein-protein
K–N · 1527 Å² buried · 24 hydrogen bonds · protein-protein
K–L · 1470 Å² buried · 15 hydrogen bonds · protein-protein
M–N · 1382 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6YBD · Structure of a human 48S translational initiation complex - eIF3 · the same entry in another collection · chain u against u, 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 Q7L2H7
Every structure of UniProt O00303
Every structure of UniProt Q14152
Every structure of UniProt P60228
Every structure of UniProt Q99613
Every structure of UniProt O15372
Every structure of UniProt P62081
Every structure of UniProt P42677
Every structure of UniProt P63220
Every structure of UniProt P08708
Every structure of UniProt P15880
Every structure of UniProt P61247
Every structure of UniProt P08865
Every structure of UniProt P62854
Every structure of UniProt P62263
Every structure of UniProt P62277
Every structure of UniProt O15371
Every structure of UniProt Q9UBQ5
Every structure of UniProt Q9Y262
Elsewhere: RCSB PDB 6YBD · PDBe 6YBD · UniProt Q7L2H7 · UniProt O00303 · UniProt Q14152 · UniProt P60228 · UniProt Q99613 · UniProt O15372 · UniProt P62081 · UniProt P42677 · UniProt P63220 · UniProt P08708 · UniProt P15880 · UniProt P61247 · UniProt P08865 · UniProt P62854 · UniProt P62263 · UniProt P62277 · UniProt O15371 · UniProt Q9UBQ5 · UniProt Q9Y262

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