Research workbench

39S large subunit of the porcine mitochondrial ribosome

Analyse 39S large subunit of the porcine mitochondrial ribosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CE4
Type: protein + RNA
Length: 5,991 residues
Chains: 38
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRPL27; MRPL28; MRPL47; MRPL30; MRPL32; MRPL33; MRPL34; MRPL35; MRPL36; 16S ribosomal…
UniProt: F1RT79, F1RGV8, F1STE5, I3LTC4, F1SVC5, I3LDE8, F1RRN2, F1RX24, F1S3J8, I3LR45, F1S286, F1RQV7, F1RSH0, F1RI89, F1RMQ4, F1SB64, I3LNJ0, F1RJD0, F1RY70, F1RHJ1, F1RW03, F1SHP6, F1SR64
Ligands: ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 37 distinct chains · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	MRPL27	protein	76	0% helix, 39% strand	F1RT79
1	MRPL28	protein	58	17% helix, 34% strand	F1RGV8
2	MRPL47	protein	76	83% helix, 0% strand	—
3	MRPL30	protein	59	37% helix, 24% strand	F1STE5
5	MRPL32	protein	68	38% helix, 9% strand	I3LTC4
6	MRPL33	protein	48	0% helix, 63% strand	—
7	MRPL34	protein	43	60% helix, 0% strand	—
8	MRPL35	protein	60	37% helix, 17% strand	F1SVC5
9	MRPL36	protein	36	8% helix, 42% strand	I3LDE8
A	16S ribosomal RNA	rna	1444	—	—
B	Unassigned RNA	rna	29	—	—
D	MRPL2	protein	200	7% helix, 32% strand	F1RRN2
E	MRPL3	protein	208	6% helix, 38% strand	F1RX24
F	MRPL4	protein	224	35% helix, 10% strand	F1S3J8
I	MRPL9	protein	57	39% helix, 16% strand	I3LR45
N	MRPL13	protein	147	31% helix, 16% strand	F1S286
O	MRPL14	protein	114	10% helix, 29% strand	F1RQV7
P	MRPL15	protein	169	28% helix, 11% strand	F1RSH0
Q	MRPL16	protein	154	32% helix, 23% strand	F1RI89
R	MRPL17	protein	120	50% helix, 16% strand	F1RMQ4
S	MRPL18	protein	94	41% helix, 20% strand	F1SB64
T	MRPL19	protein	119	26% helix, 37% strand	I3LNJ0
U	MRPL20	protein	123	79% helix, 0% strand	F1RJD0
V	MRPL21	protein	109	0% helix, 58% strand	F1RY70
W	MRPL22	protein	134	39% helix, 30% strand	—
X	MRPL23	protein	87	11% helix, 40% strand	—
Y	MRPL24	protein	103	3% helix, 48% strand	F1RHJ1
b	MRPL38	protein	192	17% helix, 29% strand	F1RW03
c	MRPL39	protein	292	41% helix, 28% strand	F1SHP6
h	MRPL44	protein	272	60% helix, 10% strand	F1SR64
i	MRPL45	protein	161	38% helix, 35% strand	—
l	MRPL49	protein	76	36% helix, 22% strand	—
o	MRPL52	protein	56	93% helix, 0% strand	—
u	ICT1	protein	90	37% helix, 22% strand	—
v, w	Unassigned helices	protein	91	86% helix, 0% strand	—
x	Thioredoxin fold	protein	85	39% helix, 24% strand	—
z	Unassigned helices	protein	426	89% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains 5, 9

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	1165	0.88	0.90	116	empty
2	1130	0.87	0.89	91	empty
3	817	0.87	0.91	77	empty
4	897	0.84	0.88	63	empty
5	650	0.84	0.89	57	empty

Interfaces

93 interfaces between chains.

A–E · 4849 Å² buried · 79 hydrogen bonds · protein-nucleic
A–P · 3850 Å² buried · 90 hydrogen bonds · protein-nucleic
A–F · 3318 Å² buried · 51 hydrogen bonds · protein-nucleic
A–D · 3144 Å² buried · 49 hydrogen bonds · protein-nucleic
A–U · 2979 Å² buried · 58 hydrogen bonds · protein-nucleic

Compared structures

4CE4 · 39S large subunit of the porcine mitochondrial ribosome · the same entry in another collection · chain 1 against 1, 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 F1RT79
Every structure of UniProt F1RGV8
Every structure of UniProt F1STE5
Every structure of UniProt I3LTC4
Every structure of UniProt F1SVC5
Every structure of UniProt I3LDE8
Every structure of UniProt F1RRN2
Every structure of UniProt F1RX24
Every structure of UniProt F1S3J8
Every structure of UniProt I3LR45
Every structure of UniProt F1S286
Every structure of UniProt F1RQV7
Every structure of UniProt F1RSH0
Every structure of UniProt F1RI89
Every structure of UniProt F1RMQ4
Every structure of UniProt F1SB64
Every structure of UniProt I3LNJ0
Every structure of UniProt F1RJD0
Every structure of UniProt F1RY70
Every structure of UniProt F1RHJ1
Every structure of UniProt F1RW03
Every structure of UniProt F1SHP6
Every structure of UniProt F1SR64
Elsewhere: RCSB PDB 4CE4 · PDBe 4CE4 · UniProt F1RT79 · UniProt F1RGV8 · UniProt F1STE5 · UniProt I3LTC4 · UniProt F1SVC5 · UniProt I3LDE8 · UniProt F1RRN2 · UniProt F1RX24 · UniProt F1S3J8 · UniProt I3LR45 · UniProt F1S286 · UniProt F1RQV7 · UniProt F1RSH0 · UniProt F1RI89 · UniProt F1RMQ4 · UniProt F1SB64 · UniProt I3LNJ0 · UniProt F1RJD0 · UniProt F1RY70 · UniProt F1RHJ1 · UniProt F1RW03 · UniProt F1SHP6 · UniProt F1SR64

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