MolNFT v1 · #170534 · protein + RNA

Mammalian 48S late-stage translation initiation complex with histone 4 mRNA

6YAN · 60S ribosomal protein L41: “Mammalian 48S late-stage translation initiation complex with histone 4 mRNA”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #170534 on GenesisL1: 3D structure, binding sites and…

PDB: 6YAN
Type: protein + RNA
Length: 7,465 residues
Chains: 39
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 60S ribosomal protein L41; 40S ribosomal protein sa; Ribosomal protein ES1; 40S ribosomal…
UniProt: A0A087WNH4, G1TLT8, G1TN72, G1TNM3, G1TK17, G1TFM5, G1TM55, G1SVB0, G1TJW1, B7NZS8, G1TPV3, G1TRM4, G1SFR8, G1SP51, G1T1F0, G1SGX4, G1TU13, G1TN62, A0A5F9CX53, G1TM82, G1TG89, G1SZ47, G1TS40, G1TFE8, G1TZ76, G1TIB4, G1U7M4, G1SK22, G1SJB4, G1TDB3, G1T8A2, G1T2G4, G1TPG3, G1U0Q2
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 39 distinct chains · 26% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
l	60S ribosomal protein L41	protein	25	92% helix, 0% strand	A0A087WNH4
C	40S ribosomal protein sa	protein	208	31% helix, 13% strand	G1TLT8
D	Ribosomal protein ES1	protein	215	27% helix, 26% strand	G1TN72
E	40S ribosomal protein US5	protein	226	31% helix, 25% strand	—
F	Ribosomal protein S3	protein	227	31% helix, 26% strand	G1TNM3
G	40S ribosomal protein S4	protein	263	12% helix, 26% strand	G1TK17
H	Ribosomal protein S5	protein	191	43% helix, 9% strand	G1TFM5
I	40S ribosomal protein S6	protein	237	27% helix, 23% strand	G1TM55
J	Ribosomal protein ES7	protein	190	32% helix, 17% strand	G1SVB0
K	40S ribosomal protein S8	protein	206	22% helix, 24% strand	G1TJW1
L	Ribosomal protein S9 (predicted)	protein	182	47% helix, 4% strand	B7NZS8
M	40S ribosomal protein ES10	protein	98	34% helix, 16% strand	G1TPV3
N	Ribosomal protein S11	protein	158	3% helix, 27% strand	G1TRM4
O	40S ribosomal protein S12	protein	124	41% helix, 7% strand	G1SFR8
P	Ribosomal protein US15	protein	150	56% helix, 0% strand	G1SP51
Q	40S ribosomal protein US11	protein	136	24% helix, 16% strand	G1T1F0
S	Ribosomal protein US9	protein	141	33% helix, 17% strand	G1SGX4
T	Ribosomal protein ES17	protein	126	47% helix, 2% strand	G1TU13
V	40S ribosomal protein ES19	protein	141	47% helix, 12% strand	G1TN62
W	RIBOSOMAL_S10 domain-containing protein	protein	104	24% helix, 36% strand	A0A5F9CX53
X	40S ribosomal protein S21	protein	82	20% helix, 29% strand	G1TM82
Y	Ribosomal protein S15A	protein	129	33% helix, 29% strand	G1TG89
Z	40S ribosomal protein US12	protein	142	20% helix, 24% strand	G1SZ47
a	40S ribosomal protein S24	protein	126	26% helix, 27% strand	G1TS40
b	40S ribosomal protein ES26	protein	99	11% helix, 22% strand	G1TFE8
c	40S ribosomal protein S27	protein	84	0% helix, 14% strand	G1TZ76
d	Ribosomal protein ES28	protein	64	0% helix, 41% strand	G1TIB4
e	Ribosomal protein US14	protein	53	19% helix, 8% strand	G1U7M4
f	Ribosomal protein ES31	protein	71	0% helix, 14% strand	G1SK22
g	Ribosomal protein RACK1	protein	313	0% helix, 51% strand	G1SJB4
h	Ribosomal protein ES25	protein	75	40% helix, 13% strand	G1TDB3
i	40S ribosomal protein ES30	protein	59	20% helix, 0% strand	G1T8A2
2	18S ribosomal RNA	rna	1744	—	—
3	Histone 4 (H4) mRNA	rna	36	—	—
A	Eukaryotic translation initiation factor 2 subunit 1	protein	266	32% helix, 16% strand	G1T2G4
B	Eukaryotic translation initiation factor 2 subunit gamma	protein	422	14% helix, 35% strand	—
U	40S ribosomal protein US13	protein	142	44% helix, 7% strand	G1TPG3
R	Ribosomal protein S15	protein	135	24% helix, 13% strand	G1U0Q2
1	Initiator methionylated tRNA	rna	75	—	—

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	739	0.87	0.92	92	empty
2	1022	0.87	0.89	92	empty
3	1003	0.86	0.88	71	empty
4	1118	0.85	0.87	83	empty
5	876	0.84	0.86	74	empty

Interfaces

113 interfaces between chains.

I–2 · 5530 Å² buried · 131 hydrogen bonds · protein-nucleic
G–2 · 4127 Å² buried · 59 hydrogen bonds · protein-nucleic
K–2 · 4004 Å² buried · 86 hydrogen bonds · protein-nucleic
L–2 · 3337 Å² buried · 67 hydrogen bonds · protein-nucleic
Z–2 · 3325 Å² buried · 59 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified, 1 disulfide (nucleotide modification, disulfide).

Compared structures

6YAN · Mammalian 48S late-stage translation initiation complex with histone 4 mRNA · the same entry in another collection · chain J against J, 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 A0A087WNH4
Every structure of UniProt G1TLT8
Every structure of UniProt G1TN72
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 G1T1F0
Every structure of UniProt G1SGX4
Every structure of UniProt G1TU13
Every structure of UniProt G1TN62
Every structure of UniProt A0A5F9CX53
Every structure of UniProt G1TM82
Every structure of UniProt G1TG89
Every structure of UniProt G1SZ47
Every structure of UniProt G1TS40
Every structure of UniProt G1TFE8
Every structure of UniProt G1TZ76
Every structure of UniProt G1TIB4
Every structure of UniProt G1U7M4
Every structure of UniProt G1SK22
Every structure of UniProt G1SJB4
Every structure of UniProt G1TDB3
Every structure of UniProt G1T8A2
Every structure of UniProt G1T2G4
Every structure of UniProt G1TPG3
Every structure of UniProt G1U0Q2
Elsewhere: RCSB PDB 6YAN · PDBe 6YAN · UniProt A0A087WNH4 · UniProt G1TLT8 · UniProt G1TN72 · UniProt G1TNM3 · UniProt G1TK17 · UniProt G1TFM5 · UniProt G1TM55 · UniProt G1SVB0 · UniProt G1TJW1 · UniProt B7NZS8 · UniProt G1TPV3 · UniProt G1TRM4 · UniProt G1SFR8 · UniProt G1SP51 · UniProt G1T1F0 · UniProt G1SGX4 · UniProt G1TU13 · UniProt G1TN62 · UniProt A0A5F9CX53 · UniProt G1TM82 · UniProt G1TG89 · UniProt G1SZ47 · UniProt G1TS40 · UniProt G1TFE8 · UniProt G1TZ76 · UniProt G1TIB4 · UniProt G1U7M4 · UniProt G1SK22 · UniProt G1SJB4 · UniProt G1TDB3 · UniProt G1T8A2 · UniProt G1T2G4 · UniProt G1TPG3 · UniProt G1U0Q2

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