Research workbench

Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and EIF1A

Analyse Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and EIF1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KZZ
Type: protein + RNA
Length: 6,859 residues
Chains: 37
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 40S ribosomal protein sa; 40S ribosomal protein S3A; 40S ribosomal protein S2; 40S…
UniProt: G1TN72, G1U2Z9, G1TNM3, G1TK17, G1TFM5, G1TM55, G1SVB0, G1TJW1, B7NZS8, G1T168, G1TRM4, G1SFR8, G1SP51, G1U472, G1U0Q2, G1SGX4, G1TU13, G1TPG3, G1TN62, G1SIZ2, G1TM82, G1TG89, G1SZ47, G1TS40, G1TDB3, G1TFE8, G1TZ76, G1TIB4, G1U7M4, G1T8A2, G1SK22, G1SJB4, P47813
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 37 distinct chains · 29% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	40S ribosomal protein sa	protein	208	34% helix, 14% strand	—
B	40S ribosomal protein S3A	protein	215	28% helix, 33% strand	G1TN72
C	40S ribosomal protein S2	protein	226	32% helix, 21% strand	G1U2Z9
D	40S ribosomal protein S3	protein	227	33% helix, 25% strand	G1TNM3
E	40S ribosomal protein S4X	protein	263	14% helix, 29% strand	G1TK17
F	40S ribosomal protein S5	protein	191	49% helix, 6% strand	G1TFM5
G	40S ribosomal protein S6	protein	237	33% helix, 24% strand	G1TM55
H	40S ribosomal protein S7	protein	190	33% helix, 21% strand	G1SVB0
I	40S ribosomal protein S8	protein	206	31% helix, 22% strand	G1TJW1
J	40S ribosomal protein S9	protein	182	46% helix, 3% strand	B7NZS8
K	40S ribosomal protein S10	protein	98	34% helix, 11% strand	G1T168
L	40S ribosomal protein S11	protein	158	3% helix, 28% strand	G1TRM4
M	40S ribosomal protein S12	protein	124	40% helix, 6% strand	G1SFR8
N	40S ribosomal protein S13	protein	150	57% helix, 0% strand	G1SP51
O	40S ribosomal protein S14	protein	136	23% helix, 21% strand	G1U472
P	40S ribosomal protein S15	protein	127	31% helix, 13% strand	G1U0Q2
Q	40S ribosomal protein S16	protein	141	34% helix, 19% strand	G1SGX4
R	40S ribosomal protein S17	protein	126	47% helix, 3% strand	G1TU13
S	40S ribosomal protein S18	protein	137	39% helix, 7% strand	G1TPG3
T	40S ribosomal protein S19	protein	141	50% helix, 9% strand	G1TN62
U	40S ribosomal protein S20	protein	104	25% helix, 42% strand	G1SIZ2
V	40S ribosomal protein S21	protein	82	18% helix, 29% strand	G1TM82
W	40S ribosomal protein S15A	protein	129	33% helix, 25% strand	G1TG89
X	40S ribosomal protein S23	protein	142	23% helix, 22% strand	G1SZ47
Y	40S ribosomal protein S24	protein	126	37% helix, 26% strand	G1TS40
Z	40S ribosomal protein S25	protein	75	35% helix, 13% strand	G1TDB3
a	40S ribosomal protein S26	protein	107	15% helix, 20% strand	G1TFE8
b	40S ribosomal protein S27	protein	84	5% helix, 14% strand	G1TZ76
c	40S ribosomal protein S28	protein	64	0% helix, 45% strand	G1TIB4
d	40S ribosomal protein S29	protein	53	32% helix, 9% strand	G1U7M4
e	40S ribosomal protein S30	protein	59	32% helix, 0% strand	G1T8A2
f	40S ribosomal protein S27A	protein	71	0% helix, 20% strand	G1SK22
g	40S ribosomal protein RACK1	protein	313	0% helix, 54% strand	G1SJB4
i	18S ribosomal RNA	rna	1797	—	—
j	Initiator met-RNA-I	rna	75	—	—
k	MRNA	rna	13	—	—
n	Human initiation factor EIF1A	protein	82	13% helix, 32% strand	P47813

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	1159	0.89	0.91	114	empty
2	847	0.87	0.91	80	empty
3	952	0.87	0.89	81	empty
4	953	0.87	0.89	97	empty
5	845	0.86	0.90	89	empty

Interfaces

104 interfaces between chains.

G–i · 4948 Å² buried · 106 hydrogen bonds · protein-nucleic
E–i · 3958 Å² buried · 59 hydrogen bonds · protein-nucleic
I–i · 3804 Å² buried · 91 hydrogen bonds · protein-nucleic
J–i · 3483 Å² buried · 59 hydrogen bonds · protein-nucleic
X–i · 3276 Å² buried · 67 hydrogen bonds · protein-nucleic

Compared structures

4KZZ · Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1A · the same entry in another collection · chain A against A, 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 G1TN72
Every structure of UniProt G1U2Z9
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 G1T168
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 G1TM82
Every structure of UniProt G1TG89
Every structure of UniProt G1SZ47
Every structure of UniProt G1TS40
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 P47813
Elsewhere: RCSB PDB 4KZZ · PDBe 4KZZ · UniProt G1TN72 · UniProt G1U2Z9 · UniProt G1TNM3 · UniProt G1TK17 · UniProt G1TFM5 · UniProt G1TM55 · UniProt G1SVB0 · UniProt G1TJW1 · UniProt B7NZS8 · UniProt G1T168 · UniProt G1TRM4 · UniProt G1SFR8 · UniProt G1SP51 · UniProt G1U472 · UniProt G1U0Q2 · UniProt G1SGX4 · UniProt G1TU13 · UniProt G1TPG3 · UniProt G1TN62 · UniProt G1SIZ2 · UniProt G1TM82 · UniProt G1TG89 · UniProt G1SZ47 · UniProt G1TS40 · UniProt G1TDB3 · UniProt G1TFE8 · UniProt G1TZ76 · UniProt G1TIB4 · UniProt G1U7M4 · UniProt G1T8A2 · UniProt G1SK22 · UniProt G1SJB4 · UniProt P47813

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