MolNFT v1 · #108251 · protein + RNA

Structure of the large subunit of the mammalian mitoribosome, part 1 of 2

4V19 · Mitoribosomal protein BL27M, MRPL27: “Structure of the large subunit of the mammalian mitoribosome, part 1 of 2”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #108251 on GenesisL1: 3D…

PDB: 4V19
Type: protein + RNA
Length: 5,944 residues
Chains: 32
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitoribosomal protein BL27M, MRPL27; Mitoribosomal protein BL28M, MRPL28; Mitoribosomal…
UniProt: F1RT79, F1RGV8, F1STE5, I3LQ65, I3LTC4, W5IDC1, F1SVC5, I3LDE8, F1RRN2, F1S3J8, I3LR45, F1RWJ0, F1RU54, F1S286, F1RQV7, F1RSH0, F1RI89, F1RMQ4, F1SB64, I3LNJ0, F1RJD0, F1RY70, F1RHJ1
Ligands: MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 31 distinct chains · 29% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	Mitoribosomal protein BL27M, MRPL27	protein	114	8% helix, 34% strand	F1RT79
1	Mitoribosomal protein BL28M, MRPL28	protein	244	44% helix, 15% strand	F1RGV8
2	Mitoribosomal protein UL29M, MRPL47	protein	178	60% helix, 7% strand	—
3	Mitoribosomal protein UL30M, MRPL30	protein	118	31% helix, 19% strand	F1STE5
4	Mitoribosomal protein BL31M, MRPL55	protein	45	0% helix, 33% strand	I3LQ65
5	Mitoribosomal protein BL32M, MRPL32	protein	110	25% helix, 13% strand	I3LTC4
6	Mitoribosomal protein BL33M, MRPL33	protein	48	0% helix, 60% strand	—
7	Mitoribosomal protein BL34M, MRPL34	protein	46	57% helix, 0% strand	W5IDC1
8	Mitoribosomal protein BL35M, MRPL35	protein	95	33% helix, 9% strand	F1SVC5
9	Mitoribosomal protein BL36M, MRPL36	protein	38	8% helix, 45% strand	I3LDE8
A	Mitoribosomal 16S rRNA	rna	1515	—	—
B	Mitoribosomal cp tRNA	rna	62	—	—
C, Z	TRNA	rna	3	—	—
D	Mitoribosomal protein UL2M, MRPL2	protein	240	6% helix, 30% strand	F1RRN2
E	Mitoribosomal protein UL3M, MRPL3	protein	307	16% helix, 27% strand	—
F	Mitoribosomal protein UL4M, MRPL4	protein	250	30% helix, 16% strand	F1S3J8
I	Mitoribosomal protein BL9M, MRPL9	protein	98	30% helix, 28% strand	I3LR45
J	Mitoribosomal protein UL10M, MRPL10	protein	168	42% helix, 13% strand	F1RWJ0
K	Mitoribosomal protein UL11M, MRPL11	protein	142	36% helix, 20% strand	F1RU54
N	Mitoribosomal protein UL13M, MRPL13	protein	177	35% helix, 14% strand	F1S286
O	Mitoribosomal protein UL14M, MRPL14	protein	115	16% helix, 32% strand	F1RQV7
P	Mitoribosomal protein UL15M, MRPL15	protein	288	30% helix, 11% strand	F1RSH0
Q	Mitoribosomal protein UL16M, MRPL16	protein	221	29% helix, 21% strand	F1RI89
R	Mitoribosomal protein BL17M, MRPL17	protein	153	46% helix, 10% strand	F1RMQ4
S	Mitoribosomal protein UL18M, MRPL18	protein	143	31% helix, 20% strand	F1SB64
T	Mitoribosomal protein BL19M, MRPL19	protein	224	30% helix, 23% strand	I3LNJ0
U	Mitoribosomal protein BL20M, MRPL20	protein	140	66% helix, 0% strand	F1RJD0
V	Mitoribosomal protein BL21M, MRPL21	protein	155	14% helix, 44% strand	F1RY70
W	Mitoribosomal protein UL22M, MRPL22	protein	166	34% helix, 25% strand	—
X	Mitoribosomal protein UL23M, MRPL23	protein	134	9% helix, 22% strand	—
Y	Mitoribosomal protein UL24M, MRPL24	protein	204	11% helix, 28% strand	F1RHJ1

Ligands and binding sites

MG · Magnesium ion · metal · 169 copies · chains A, X, P, D, E, F, U, T, R, 0, I, Z, W, 8, Q
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	1021	0.88	0.91	78	MG
2	962	0.88	0.91	94	MG
3	1070	0.86	0.88	96	MG
4	759	0.85	0.90	74	MG
5	1131	0.84	0.86	84	MG

Interfaces

75 interfaces between chains.

A–E · 5497 Å² buried · 94 hydrogen bonds · protein-nucleic
A–D · 4860 Å² buried · 122 hydrogen bonds · protein-nucleic
A–P · 4144 Å² buried · 107 hydrogen bonds · protein-nucleic
A–F · 3560 Å² buried · 50 hydrogen bonds · protein-nucleic
A–U · 3244 Å² buried · 74 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 62 modified (nucleotide modification).

Compared structures

4V19 · Structure of the large subunit of the mammalian mitoribosome, part 1 of 2 · 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 I3LQ65
Every structure of UniProt I3LTC4
Every structure of UniProt W5IDC1
Every structure of UniProt F1SVC5
Every structure of UniProt I3LDE8
Every structure of UniProt F1RRN2
Every structure of UniProt F1S3J8
Every structure of UniProt I3LR45
Every structure of UniProt F1RWJ0
Every structure of UniProt F1RU54
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
Elsewhere: RCSB PDB 4V19 · PDBe 4V19 · UniProt F1RT79 · UniProt F1RGV8 · UniProt F1STE5 · UniProt I3LQ65 · UniProt I3LTC4 · UniProt W5IDC1 · UniProt F1SVC5 · UniProt I3LDE8 · UniProt F1RRN2 · UniProt F1S3J8 · UniProt I3LR45 · UniProt F1RWJ0 · UniProt F1RU54 · UniProt F1S286 · UniProt F1RQV7 · UniProt F1RSH0 · UniProt F1RI89 · UniProt F1RMQ4 · UniProt F1SB64 · UniProt I3LNJ0 · UniProt F1RJD0 · UniProt F1RY70 · UniProt F1RHJ1

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