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Structure of the delta dii ires EIF5B-containing 48S initiation complex, closed conformation. structure 15(DELTA dii)

Analyse Structure of the delta dii ires EIF5B-containing 48S initiation complex, closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SYX
Type: protein + RNA
Length: 7,582 residues
Chains: 39
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S rRNA; Eukaryotic translation initiation factor 1A, X-chromosomal; US2; ES1; US5; US3…
UniProt: P47813, G1TLT8, G1SS70, G1TNM3, G1TK17, G1TFM5, G1TM55, G1SVB0, G1TJW1, B7NZS8, G1TPV3, G1TRM4, G1SFR8, G1SP51, G1U472, G1U0Q2, G1SGX4, G1TU13, G1TPG3, G1TN62, G1SIZ2, G1TG89, G1SZ47, G1T3D8, G1TDB3, G1TFE8, G1TZ76, G1TIB4, G1U7M4, G1T8A2, G1SK22, G1SJB4, A0A087WNH4, G1TRL5
Ligands: GTP, ZN, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 39 distinct chains · 28% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S rRNA	rna	1697	—	—
A	Eukaryotic translation initiation factor 1A, X-chromosomal	protein	99	13% helix, 30% strand	P47813
B	US2	protein	217	37% helix, 13% strand	G1TLT8
C	ES1	protein	213	24% helix, 29% strand	G1SS70
D	US5	protein	221	32% helix, 27% strand	—
E	US3	protein	228	33% helix, 26% strand	G1TNM3
F	ES4	protein	262	13% helix, 27% strand	G1TK17
G	US7	protein	191	48% helix, 7% strand	G1TFM5
H	ES6	protein	237	28% helix, 19% strand	G1TM55
I	40S ribosomal protein S7	protein	185	34% helix, 21% strand	G1SVB0
J	ES8	protein	206	25% helix, 24% strand	G1TJW1
K	US4	protein	185	50% helix, 5% strand	B7NZS8
L	ES10	protein	96	39% helix, 6% strand	G1TPV3
M	US17	protein	151	3% helix, 28% strand	G1TRM4
N	ES12	protein	117	38% helix, 9% strand	G1SFR8
O	US15	protein	149	50% helix, 0% strand	G1SP51
P	US11	protein	136	23% helix, 27% strand	G1U472
Q	US19	protein	120	28% helix, 14% strand	G1U0Q2
R	US9	protein	142	37% helix, 18% strand	G1SGX4
S	ES17	protein	132	42% helix, 5% strand	G1TU13
T	US13	protein	144	38% helix, 9% strand	G1TPG3
U	ES19	protein	141	49% helix, 11% strand	G1TN62
V	US10	protein	100	24% helix, 33% strand	G1SIZ2
W	ES21	protein	83	22% helix, 27% strand	—
X	US8	protein	129	30% helix, 26% strand	G1TG89
Y	US12	protein	141	20% helix, 27% strand	G1SZ47
Z	40S ribosomal protein S24	protein	124	31% helix, 29% strand	G1T3D8
a	40S ribosomal protein S25	protein	77	44% helix, 14% strand	G1TDB3
b	ES26	protein	101	14% helix, 24% strand	G1TFE8
c	ES27	protein	83	7% helix, 17% strand	G1TZ76
d	ES28	protein	67	0% helix, 40% strand	G1TIB4
e	ES29	protein	55	24% helix, 9% strand	G1U7M4
f	ES30	protein	57	26% helix, 0% strand	G1T8A2
g	40S ribosomal protein S27A	protein	68	4% helix, 18% strand	G1SK22
h	RACK1	protein	313	0% helix, 46% strand	G1SJB4
i	Met-tRNA-I-met	rna	75	—	—
n	60S ribosomal protein L41	protein	25	84% helix, 0% strand	A0A087WNH4
x	Eukaryotic translation initiation factor 5B	protein	627	30% helix, 22% strand	G1TRL5
z	HCV ires	rna	188	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains x
ZN · Zinc ion · metal · chains b
MG · Magnesium ion · metal · chains x

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	1093	0.88	0.91	89	empty
2	987	0.88	0.90	90	empty
3	1037	0.88	0.90	93	empty
4	914	0.88	0.91	82	empty
5	998	0.87	0.89	105	empty

Interfaces

116 interfaces between chains.

2–H · 5256 Å² buried · 87 hydrogen bonds · protein-nucleic
2–J · 4299 Å² buried · 84 hydrogen bonds · protein-nucleic
2–F · 3751 Å² buried · 60 hydrogen bonds · protein-nucleic
2–K · 3651 Å² buried · 59 hydrogen bonds · protein-nucleic
2–Y · 3465 Å² buried · 79 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7SYX · Structure of the delta dII IRES eIF5B-containing 48S initiation complex, closed… · the same entry in another collection · chain 2 against 2, 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 P47813
Every structure of UniProt G1TLT8
Every structure of UniProt G1SS70
Every structure of UniProt G1TNM3
Every structure of UniProt G1TK17
Every structure of UniProt G1TFM5
Every structure of UniProt G1TM55
Every structure of UniProt G1SVB0
Every structure of UniProt G1TJW1
Every structure of UniProt B7NZS8
Every structure of UniProt G1TPV3
Every structure of UniProt G1TRM4
Every structure of UniProt G1SFR8
Every structure of UniProt G1SP51
Every structure of UniProt G1U472
Every structure of UniProt G1U0Q2
Every structure of UniProt G1SGX4
Every structure of UniProt G1TU13
Every structure of UniProt G1TPG3
Every structure of UniProt G1TN62
Every structure of UniProt G1SIZ2
Every structure of UniProt G1TG89
Every structure of UniProt G1SZ47
Every structure of UniProt G1T3D8
Every structure of UniProt G1TDB3
Every structure of UniProt G1TFE8
Every structure of UniProt G1TZ76
Every structure of UniProt G1TIB4
Every structure of UniProt G1U7M4
Every structure of UniProt G1T8A2
Every structure of UniProt G1SK22
Every structure of UniProt G1SJB4
Every structure of UniProt A0A087WNH4
Every structure of UniProt G1TRL5
Elsewhere: RCSB PDB 7SYX · PDBe 7SYX · UniProt P47813 · UniProt G1TLT8 · UniProt G1SS70 · UniProt G1TNM3 · UniProt G1TK17 · UniProt G1TFM5 · UniProt G1TM55 · UniProt G1SVB0 · UniProt G1TJW1 · UniProt B7NZS8 · UniProt G1TPV3 · UniProt G1TRM4 · UniProt G1SFR8 · UniProt G1SP51 · UniProt G1U472 · UniProt G1U0Q2 · UniProt G1SGX4 · UniProt G1TU13 · UniProt G1TPG3 · UniProt G1TN62 · UniProt G1SIZ2 · UniProt G1TG89 · UniProt G1SZ47 · UniProt G1T3D8 · UniProt G1TDB3 · UniProt G1TFE8 · UniProt G1TZ76 · UniProt G1TIB4 · UniProt G1U7M4 · UniProt G1T8A2 · UniProt G1SK22 · UniProt G1SJB4 · UniProt A0A087WNH4 · UniProt G1TRL5

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