Research workbench

Human mitochondrial ribosome in complex with mRNA and P-site tRNA

Analyse Human mitochondrial ribosome in complex with mRNA and P-site tRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZSB
Type: protein + RNA
Length: 16,597 residues
Chains: 92
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.5
Source: Homo sapiens
Molecule: 39S ribosomal protein L32, mitochondrial; 39S ribosomal protein L33, mitochondrial; 39S…
EC: 3.1.26.-, 3.1.1.29
UniProt: Q9BYC8, O75394, Q9BQ48, Q9NZE8, Q9P0J6, Q9BZE1, Q96DV4, Q9NYK5, Q9NQ50, Q8IXM3, P82930, P82673, Q96BP2, Q9NWT8, Q96EY7, Q9Y399, Q96EL2, P82675, P82932, Q9Y2R9, P82933, P82664, P82912, O15235, O60783, P82914, Q9Y3D3, Q9Y2R5, Q9Y676, Q9Y3D5, P82921, P82650, Q9Y3D9, P82663, Q9BYN8, Q92552, Q9Y2Q9, P51398, Q92665, Q9Y291, Q5T653, P09001, Q9BYD3, Q9BYD2, Q7Z7H8, Q9Y3B7, Q9BYD1, Q6P1L8, Q9P015, Q9NX20, Q9NRX2, Q9H0U6, P49406, Q9BYC9, Q7Z2W9, Q9NWU5, Q16540, Q96A35, Q9P0M9, Q13084, Q9HD33, Q8TCC3, Q9Y6G3, Q8N983, Q9H9J2, Q9BRJ2, Q9H2W6, Q96GC5, Q13405, Q8N5N7, Q4U2R6, Q86TS9, Q96EL3, Q6P161, Q7Z7F7, Q9BQC6, Q14197, Q8TAE8, Q9NVS2, Q9NP92, P52815
Ligands: DOL, GTP, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 4.5 · 90 distinct chains · 38% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	39S ribosomal protein L32, mitochondrial	protein	108	29% helix, 13% strand	Q9BYC8
1	39S ribosomal protein L33, mitochondrial	protein	53	0% helix, 64% strand	O75394
2	39S ribosomal protein L34, mitochondrial	protein	46	57% helix, 0% strand	Q9BQ48
3	39S ribosomal protein L35, mitochondrial	protein	95	33% helix, 12% strand	Q9NZE8
4	39S ribosomal protein L36, mitochondrial	protein	38	8% helix, 39% strand	Q9P0J6
5	39S ribosomal protein L37, mitochondrial	protein	393	26% helix, 18% strand	Q9BZE1
6	39S ribosomal protein L38, mitochondrial	protein	354	27% helix, 16% strand	Q96DV4
7	39S ribosomal protein L39, mitochondrial	protein	291	38% helix, 21% strand	Q9NYK5
8	39S ribosomal protein L40, mitochondrial	protein	139	56% helix, 9% strand	Q9NQ50
9	39S ribosomal protein L41, mitochondrial	protein	124	23% helix, 9% strand	Q8IXM3
XA	16S mitochondrial rRNA	rna	1499	—	—
A0	28S ribosomal protein S34, mitochondrial	protein	201	32% helix, 20% strand	P82930
A1	28S ribosomal protein S35, mitochondrial	protein	275	40% helix, 8% strand	P82673
A2	Coiled-coil-helix-coiled-coil-helix domain-containing protein 1	protein	116	47% helix, 0% strand	Q96BP2
A3	Aurora kinase A-interacting protein	protein	69	71% helix, 0% strand	Q9NWT8
A4	Pentatricopeptide repeat domain-containing protein 3, mitochondrial	protein	552	66% helix, 1% strand	Q96EY7
AA	12S mitochondrial rRNA	rna	924	—	—
AB	28S ribosomal protein S2, mitochondrial	protein	218	47% helix, 15% strand	Q9Y399
AC	28S ribosomal protein S24, mitochondrial	protein	132	33% helix, 20% strand	Q96EL2
AD	28S ribosomal protein S5, mitochondrial	protein	343	25% helix, 20% strand	P82675
AE	28S ribosomal protein S6, mitochondrial	protein	122	25% helix, 39% strand	P82932
AF	28S ribosomal protein S7, mitochondrial	protein	201	56% helix, 8% strand	Q9Y2R9
AG	28S ribosomal protein S9, mitochondrial	protein	304	45% helix, 12% strand	P82933
AH	28S ribosomal protein S10, mitochondrial	protein	135	23% helix, 42% strand	P82664
AI	28S ribosomal protein S11, mitochondrial	protein	136	27% helix, 23% strand	P82912
AJ	28S ribosomal protein S12, mitochondrial	protein	108	6% helix, 31% strand	O15235
AK	28S ribosomal protein S14, mitochondrial	protein	101	50% helix, 3% strand	O60783
AL	28S ribosomal protein S15, mitochondrial	protein	164	65% helix, 1% strand	P82914
AM	28S ribosomal protein S16, mitochondrial	protein	116	38% helix, 28% strand	Q9Y3D3
AN	28S ribosomal protein S17, mitochondrial	protein	107	0% helix, 40% strand	Q9Y2R5
AO	28S ribosomal protein S18b, mitochondrial	protein	185	31% helix, 1% strand	Q9Y676
AP	28S ribosomal protein S18c, mitochondrial	protein	95	32% helix, 1% strand	Q9Y3D5
AQ	28S ribosomal protein S21, mitochondrial	protein	85	64% helix, 4% strand	P82921
AR	28S ribosomal protein S22, mitochondrial	protein	250	50% helix, 7% strand	P82650
AS	28S ribosomal protein S23, mitochondrial	protein	133	46% helix, 2% strand	Q9Y3D9
AT	28S ribosomal protein S25, mitochondrial	protein	162	34% helix, 13% strand	P82663
AU	28S ribosomal protein S26, mitochondrial	protein	173	72% helix, 2% strand	Q9BYN8
AV	28S ribosomal protein S27, mitochondrial	protein	349	72% helix, 0% strand	Q92552
AW	28S ribosomal protein S28, mitochondrial	protein	97	11% helix, 33% strand	Q9Y2Q9
AX	28S ribosomal protein S29, mitochondrial	protein	348	42% helix, 13% strand	P51398
AY	28S ribosomal protein S31, mitochondrial	protein	113	58% helix, 0% strand	Q92665
AZ	28S ribosomal protein S33, mitochondrial	protein	86	69% helix, 0% strand	Q9Y291
XB	mitochondrial tRNAVal	rna	59	—	—
XD	39S ribosomal protein L2, mitochondrial	protein	236	4% helix, 28% strand	Q5T653
XE	39S ribosomal protein L3, mitochondrial	protein	304	14% helix, 27% strand	P09001
XF	39S ribosomal protein L4, mitochondrial	protein	250	30% helix, 12% strand	Q9BYD3
XH	39S ribosomal protein L9, mitochondrial	protein	95	26% helix, 25% strand	Q9BYD2
XI	39S ribosomal protein L10, mitochondrial	protein	211	48% helix, 9% strand	Q7Z7H8
XJ	39S ribosomal protein L11, mitochondrial	protein	170	49% helix, 12% strand	Q9Y3B7
XK	39S ribosomal protein L13, mitochondrial	protein	177	36% helix, 15% strand	Q9BYD1
XL	39S ribosomal protein L14, mitochondrial	protein	115	11% helix, 29% strand	Q6P1L8
XM	39S ribosomal protein L15, mitochondrial	protein	287	31% helix, 11% strand	Q9P015
XN	39S ribosomal protein L16, mitochondrial	protein	221	25% helix, 20% strand	Q9NX20
XO	39S ribosomal protein L17, mitochondrial	protein	152	49% helix, 11% strand	Q9NRX2
XP	39S ribosomal protein L18, mitochondrial	protein	143	31% helix, 18% strand	Q9H0U6
XQ	39S ribosomal protein L19, mitochondrial	protein	238	25% helix, 21% strand	P49406
XR	39S ribosomal protein L20, mitochondrial	protein	140	66% helix, 1% strand	Q9BYC9
XS	39S ribosomal protein L21, mitochondrial	protein	160	13% helix, 39% strand	Q7Z2W9
XT	39S ribosomal protein L22, mitochondrial	protein	166	37% helix, 25% strand	Q9NWU5
XU	39S ribosomal protein L23, mitochondrial	protein	141	18% helix, 21% strand	Q16540
XV	39S ribosomal protein L24, mitochondrial	protein	202	10% helix, 23% strand	Q96A35
XW	39S ribosomal protein L27, mitochondrial	protein	111	8% helix, 36% strand	Q9P0M9
XX	39S ribosomal protein L28, mitochondrial	protein	243	44% helix, 14% strand	Q13084
XY	39S ribosomal protein L47, mitochondrial	protein	178	58% helix, 7% strand	Q9HD33
XZ	39S ribosomal protein L30, mitochondrial	protein	120	30% helix, 18% strand	Q8TCC3
a	39S ribosomal protein L42, mitochondrial	protein	97	22% helix, 11% strand	Q9Y6G3
b	39S ribosomal protein L43, mitochondrial	protein	148	22% helix, 20% strand	Q8N983
c	39S ribosomal protein L44, mitochondrial (EC 3.1.26.-)	protein	275	57% helix, 9% strand	Q9H9J2
d	39S ribosomal protein L45, mitochondrial	protein	216	24% helix, 25% strand	Q9BRJ2
e	39S ribosomal protein L46, mitochondrial	protein	217	39% helix, 19% strand	Q9H2W6
f	39S ribosomal protein L48, mitochondrial	protein	143	33% helix, 34% strand	Q96GC5
g	39S ribosomal protein L49, mitochondrial	protein	132	28% helix, 24% strand	Q13405
h	39S ribosomal protein L50, mitochondrial	protein	108	43% helix, 6% strand	Q8N5N7
i	39S ribosomal protein L51, mitochondrial	protein	97	41% helix, 1% strand	Q4U2R6
j	39S ribosomal protein L52, mitochondrial	protein	86	67% helix, 2% strand	Q86TS9
k	39S ribosomal protein L53, mitochondrial	protein	95	38% helix, 24% strand	Q96EL3
l	39S ribosomal protein L54, mitochondrial	protein	80	40% helix, 0% strand	Q6P161
m	39S ribosomal protein L55, mitochondrial	protein	60	15% helix, 25% strand	Q7Z7F7
o	Ribosomal protein 63, mitochondrial	protein	94	51% helix, 1% strand	Q9BQC6
p	Peptidyl-tRNA hydrolase ICT1, mitochondrial (EC 3.1.1.29)	protein	127	41% helix, 17% strand	Q14197
q	Growth arrest and DNA damage-inducible proteins-interacting protein 1	protein	164	71% helix, 0% strand	Q8TAE8
r	39S ribosomal protein S18a, mitochondrial	protein	152	27% helix, 12% strand	Q9NVS2
r1	mRNA	rna	4	—	—
r3	P-site tRNA	rna	75	—	—
s	39S ribosomal protein S30, mitochondrial	protein	370	34% helix, 21% strand	Q9NP92
t1	39S ribosomal protein L12, mitochondrial	protein	46	57% helix, 0% strand	P52815
t2, t3	39S ribosomal protein L12, mitochondrial	protein	30	80% helix, 0% strand	P52815
t4, t5	39S ribosomal protein L12, mitochondrial	protein	29	83% helix, 0% strand	P52815
t6	39S ribosomal protein L12, mitochondrial	protein	27	85% helix, 4% strand	P52815
A	Quinupristin	protein	7	0% helix, 0% strand	—

Ligands and binding sites

DOL · 5-(2-diethylamino-ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone · ligand · chains XA, r3, A
GTP · Guanosine-5'-triphosphate · ligand · chains AX
MG · Magnesium ion · metal · 195 copies · chains 9, XA, XF, XS, XM, XE, XI, XR, XU, s, XO, XQ, XL, XD, o, XW, r, A2, AA, AD, AJ, AQ, AH, AK, g
ZN · Zinc ion · metal · 7 copies · chains 0, 4, AB, AO, AE, AP, AT, XI, r

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	982	0.89	0.91	124	empty
2	898	0.88	0.90	89	empty
3	993	0.87	0.88	95	empty
4	923	0.87	0.89	71	empty
5	992	0.87	0.89	88	MG

Interfaces

352 interfaces between chains.

XA–XE · 5169 Å² buried · 76 hydrogen bonds · protein-nucleic
XA–XD · 4855 Å² buried · 103 hydrogen bonds · protein-nucleic
XA–XM · 4094 Å² buried · 102 hydrogen bonds · protein-nucleic
AA–AD · 3606 Å² buried · 71 hydrogen bonds · protein-nucleic
XA–XF · 3567 Å² buried · 51 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 84 modified (nucleotide modification, nonstandard).

Compared structures

Q9Y399 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S2, mitochondrial (Q9Y399) · a predicted model of the same protein · chain AB against A, TM-score 0.99
Q9NP92 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein S30, mitochondrial (Q9NP92) · a predicted model of the same protein · chain s against A, TM-score 0.99
Q5T653 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L2, mitochondrial (Q5T653) · a predicted model of the same protein · chain XD against A, TM-score 0.99
Q9H9J2 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L44, mitochondrial (Q9H9J2) · a predicted model of the same protein · chain c against A, TM-score 0.98
P09001 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L3, mitochondrial (P09001) · a predicted model of the same protein · chain XE against A, TM-score 0.98
Q9NYK5 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L39, mitochondrial (Q9NYK5) · a predicted model of the same protein · chain 7 against A, TM-score 0.98
Q9BYD3 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L4, mitochondrial (Q9BYD3) · a predicted model of the same protein · chain XF against A, TM-score 0.98
Q9BZE1 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L37, mitochondrial (Q9BZE1) · a predicted model of the same protein · chain 5 against A, TM-score 0.98
Q9BRJ2 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L45, mitochondrial (Q9BRJ2) · a predicted model of the same protein · chain d against A, TM-score 0.98
Q13084 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L28, mitochondrial (Q13084) · a predicted model of the same protein · chain XX against A, TM-score 0.98
Q9NX20 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L16, mitochondrial (Q9NX20) · a predicted model of the same protein · chain XN against A, TM-score 0.98
Q8N983 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L43, mitochondrial (Q8N983) · a predicted model of the same protein · chain b against A, TM-score 0.98

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.