MolNFT v1 · #108252 · protein

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

4V1A · Mitoribosomal protein ML37, MRPL37: “Structure of the large subunit of the mammalian mitoribosome, part 2 of 2”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.73). MolNFT v1 #108252 on GenesisL1: 3D structure…

PDB: 4V1A
Type: protein
Length: 3,936 residues
Chains: 23
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitoribosomal protein ML37, MRPL37; Mitoribosomal protein ML38, MRPL38; Mitoribosomal…
UniProt: F1RW03, F1RK59, F1S8U4, F1SR64, F1SRT0, I3L9H6, F1S9B7, F1SLH8, W5IDC0, F1SD95, F1RRH6
Ligands: ZN
Pockets: 20 · best druggability 0.73

Structure

electron microscopy · 23 distinct chains · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	Mitoribosomal protein ML37, MRPL37	protein	393	27% helix, 26% strand	—
b	Mitoribosomal protein ML38, MRPL38	protein	354	25% helix, 18% strand	F1RW03
c	Mitoribosomal protein ML39, MRPL39	protein	295	34% helix, 27% strand	—
d	Mitoribosomal protein ML40, MRPL40	protein	99	62% helix, 4% strand	F1RK59
e	Mitoribosomal protein ML41, MRPL41	protein	121	19% helix, 5% strand	—
f	Mitoribosomal protein ML42, MRPL42	protein	108	23% helix, 11% strand	—
g	Mitoribosomal protein ML43, MRPL43	protein	148	26% helix, 18% strand	F1S8U4
h	Mitoribosomal protein ML44, MRPL44	protein	289	58% helix, 9% strand	F1SR64
i	Mitoribosomal protein ML45, MRPL45	protein	242	26% helix, 24% strand	—
j	Mitoribosomal protein ML46, MRPL46	protein	217	33% helix, 29% strand	F1SRT0
k	Mitoribosomal protein ML48, MRPL48	protein	131	23% helix, 36% strand	—
l	Mitoribosomal protein ML49, MRPL49	protein	133	25% helix, 20% strand	—
m	Mitoribosomal protein ML50, MRPL50	protein	109	41% helix, 6% strand	I3L9H6
n	Mitoribosomal protein ML51, MRPL51	protein	97	47% helix, 0% strand	—
o	Mitoribosomal protein ML52, MRPL52	protein	94	63% helix, 0% strand	F1S9B7
p	Mitoribosomal protein ML53, MRPL53	protein	97	36% helix, 27% strand	F1SLH8
q	Mitoribosomal protein ML54, MRPL54	protein	37	38% helix, 0% strand	—
t	Mitoribosomal protein ML63, MRPL57, MRP63	protein	94	50% helix, 1% strand	—
u	Mitoribosomal protein ML62, MRPL58, ICT1	protein	151	36% helix, 17% strand	W5IDC0
v	Mitoribosomal protein ML64, MRPL59, CRIF1	protein	131	68% helix, 0% strand	F1SD95
w	Mitoribosomal protein ML65, MRPS30	protein	387	34% helix, 22% strand	—
x	Mitoribosomal protein ML66, MRPS18A	protein	162	23% helix, 11% strand	F1RRH6
z	Unassigned secondary structure elements	protein	47	70% helix, 6% strand	—

Ligands and binding sites

ZN · Zinc 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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	876	0.73	0.77	78	empty
2	507	0.72	0.81	66	empty
3	534	0.70	0.79	49	empty
4	365	0.70	0.82	38	empty
5	164	0.67	0.87	25	empty

Interfaces

29 interfaces between chains.

d–j · 2222 Å² buried · 28 hydrogen bonds · protein-protein
g–h · 1568 Å² buried · 21 hydrogen bonds · protein-protein
a–w · 1507 Å² buried · 14 hydrogen bonds · protein-protein
d–k · 1412 Å² buried · 12 hydrogen bonds · protein-protein
b–u · 1139 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4V1A · Structure of the large subunit of the mammalian mitoribosome, part 2 of 2 · 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 F1RW03
Every structure of UniProt F1RK59
Every structure of UniProt F1S8U4
Every structure of UniProt F1SR64
Every structure of UniProt F1SRT0
Every structure of UniProt I3L9H6
Every structure of UniProt F1S9B7
Every structure of UniProt F1SLH8
Every structure of UniProt W5IDC0
Every structure of UniProt F1SD95
Every structure of UniProt F1RRH6
Elsewhere: RCSB PDB 4V1A · PDBe 4V1A · UniProt F1RW03 · UniProt F1RK59 · UniProt F1S8U4 · UniProt F1SR64 · UniProt F1SRT0 · UniProt I3L9H6 · UniProt F1S9B7 · UniProt F1SLH8 · UniProt W5IDC0 · UniProt F1SD95 · UniProt F1RRH6

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