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Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic CC-Pmn and bound to mRNA and P-site tRNA at 3.7A resolution

Analyse Crystal structure of the Thermus thermophilus 70S ribosome in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6N9E
Type: protein + RNA
Length: 20,651 residues
Chains: 110
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.7
Source: Escherichia coli; Thermus thermophilus; SYNTHETIC CONSTRUCT
Molecule: 23S Ribosomal RNA; 5S Ribosomal RNA; 50S Ribosomal Protein L2; 50S Ribosomal Protein L3…
UniProt: Q56435, Q72IA7, P60493, P60494, Q72I12, P74909, Q72JR0, P80339, Q72GW3, P80340, P80374, P80375, P62654, P17293, P62655, P24320, P80378, P62238, P0DOY7, P62659, P62612
Ligands: SF4, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · resolution 3.7 · 60 distinct chains · 29% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1A	23S Ribosomal RNA	rna	2871	—	—
1B, 2B	5S Ribosomal RNA	rna	120	—	—
1D, 2D	50S Ribosomal Protein L2	protein	275	10% helix, 27% strand	—
1E, 2E	50S Ribosomal Protein L3	protein	204	11% helix, 41% strand	—
1F, 2F	50S Ribosomal Protein L4	protein	202	34% helix, 14% strand	—
1G, 2G	50S Ribosomal Protein L5	protein	181	31% helix, 20% strand	—
1H, 2H	50S Ribosomal Protein L6	protein	174	20% helix, 37% strand	—
1I, 2I	50S Ribosomal Protein L9	protein	146	37% helix, 32% strand	—
1N, 2N	50S Ribosomal Protein L13	protein	140	29% helix, 19% strand	—
1O, 2O	50S Ribosomal Protein L14	protein	122	8% helix, 40% strand	—
1P, 2P	50S Ribosomal Protein L15	protein	149	17% helix, 15% strand	—
1Q, 2Q	50S Ribosomal Protein L16	protein	141	24% helix, 27% strand	—
1R, 2R	50S Ribosomal Protein L17	protein	118	53% helix, 14% strand	—
1S, 2S	50S Ribosomal Protein L18	protein	110	42% helix, 22% strand	—
1T, 2T	50S Ribosomal Protein L19	protein	131	26% helix, 39% strand	—
1U, 2U	50S Ribosomal Protein L20	protein	116	76% helix, 0% strand	—
1V, 2V	50S Ribosomal Protein L21	protein	101	0% helix, 60% strand	—
1W, 2W	50S Ribosomal Protein L22	protein	112	38% helix, 37% strand	—
1X, 2X	50S Ribosomal Protein L23	protein	95	25% helix, 37% strand	—
1Y, 2Y	50S ribosomal protein L24	protein	107	3% helix, 43% strand	Q56435
1Z	50S ribosomal protein L25	protein	154	13% helix, 42% strand	Q72IA7
10, 20	50S ribosomal protein L27	protein	83	4% helix, 35% strand	P60493
11, 21	50S ribosomal protein L28	protein	97	24% helix, 36% strand	P60494
12, 22	50S ribosomal protein L29	protein	70	80% helix, 0% strand	Q72I12
13, 23	50S ribosomal protein L30	protein	59	37% helix, 29% strand	P74909
14, 24	50S ribosomal protein L31	protein	69	0% helix, 22% strand	Q72JR0
15, 25	50S ribosomal protein L32	protein	59	17% helix, 12% strand	P80339
16, 26	50S ribosomal protein L33	protein	53	0% helix, 60% strand	Q72GW3
17, 27	50S ribosomal protein L34	protein	48	52% helix, 0% strand	P80340
18, 28	50S Ribosomal Protein L35	protein	64	31% helix, 14% strand	—
19, 29	50S Ribosomal Protein L36	protein	37	8% helix, 32% strand	—
1a	16S Ribosomal RNA	rna	1499	—	—
1b, 2b	30S Ribosomal Protein S2	protein	231	47% helix, 11% strand	—
1c, 2c	30S Ribosomal Protein S3	protein	206	34% helix, 25% strand	—
1d, 2d	30S Ribosomal Protein S4	protein	208	43% helix, 10% strand	—
1e, 2e	30S Ribosomal Protein S5	protein	148	28% helix, 39% strand	—
1f, 2f	30S Ribosomal Protein S6	protein	100	28% helix, 44% strand	—
1g, 2g	30S Ribosomal Protein S7	protein	155	57% helix, 5% strand	—
1h, 2h	30S Ribosomal Protein S8	protein	137	28% helix, 28% strand	—
1i, 2i	30S ribosomal protein S9	protein	127	26% helix, 23% strand	P80374
1j	30S ribosomal protein S10	protein	97	22% helix, 43% strand	P80375
1k, 2k	30S ribosomal protein S11	protein	114	29% helix, 28% strand	P62654
1l, 2l	30S ribosomal protein S12	protein	122	7% helix, 30% strand	P17293
1m	30S ribosomal protein S13	protein	123	49% helix, 2% strand	P62655
1n, 2n	30S ribosomal protein S14 type Z	protein	60	30% helix, 12% strand	P24320
1o, 2o	30S ribosomal protein S15	protein	88	75% helix, 0% strand	P80378
1p, 2p	30S ribosomal protein S16	protein	82	22% helix, 34% strand	P62238
1q, 2q	30S ribosomal protein S17	protein	99	17% helix, 44% strand	P0DOY7
1r, 2r	30S ribosomal protein S18	protein	68	37% helix, 9% strand	P62659
1s, 2s	30S Ribosomal Protein S19	protein	83	20% helix, 18% strand	—
1t, 2t	30S Ribosomal Protein S20	protein	96	77% helix, 0% strand	—
1u, 2u	30S ribosomal protein Thx	protein	23	30% helix, 0% strand	P62612
1v, 2v	mRNA	rna	5	—	—
1w, 2w	CC-Pmn	rna	2	—	—
1x, 2x	P-site tRNA, Deacylated Initiator Methionyl-tRNA	rna	76	—	—
2A	23S Ribosomal RNA	rna	2800	—	—
2Z	50S ribosomal protein L25	protein	160	13% helix, 44% strand	Q72IA7
2a	16S Ribosomal RNA	rna	1503	—	—
2j	30S ribosomal protein S10	protein	96	21% helix, 41% strand	P80375
2m	30S ribosomal protein S13	protein	122	49% helix, 2% strand	P62655

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 2 copies · chains 1d, 2d
MG · Magnesium ion · metal · 1156 copies · chains 1A, 19, 1D, 12, 1P, 17, 1F, 1H, 1B, 13, 1V, 16, 1R, 1Y, 1T, 1Q, 1X, 1E, 11, 1U, 18, 1N, 1a, 1S, 1W, 10, 15, 1t, 1q, 1u, 1d, 1h, 1e, 1m, 1l, 1i, 1o, 1v, 1f, 1r, 1x, 2A, 2R, 2I, 29, 2P, 2F, 28, 2D, 2W, 2X, 2a, 2O, 21, 2T, 2E, 20, 2U, 2V, 2B, 2Q, 25, 2Y, 23, 27, 2i, 2l, 2c, 2k, 2x, 2p, 2o, 2e, 2v, 2d, 2f, 2r
ZN · Zinc ion · metal · 12 copies · chains 1Y, 14, 15, 16, 19, 1n, 2Y, 24, 25, 26, 29, 2n

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	951	0.89	0.92	91	MG
2	930	0.89	0.92	85	MG
3	1451	0.89	0.91	129	MG
4	1449	0.88	0.91	126	MG
5	1395	0.88	0.91	123	MG

Interfaces

250 interfaces between chains.

1A–1D · 7603 Å² buried · 218 hydrogen bonds · protein-nucleic
2A–2D · 7523 Å² buried · 214 hydrogen bonds · protein-nucleic
1A–1E · 5365 Å² buried · 146 hydrogen bonds · protein-nucleic
2A–2E · 5341 Å² buried · 149 hydrogen bonds · protein-nucleic
1A–1P · 5243 Å² buried · 135 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 56 modified, 5 covalent (nucleotide modification, covalent ligand, nonstandard).

Compared structures

P17293 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S12 (P17293) · a predicted model of the same protein · chain 1l against A, TM-score 0.98
P62238 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S16 (P62238) · a predicted model of the same protein · chain 1p against A, TM-score 0.97
P62659 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S18 (P62659) · a predicted model of the same protein · chain 1r against A, TM-score 0.97
Q72IA7 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L25 (Q72IA7) · a predicted model of the same protein · chain 1Z against A, TM-score 0.97
Q72I12 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L29 (Q72I12) · a predicted model of the same protein · chain 12 against A, TM-score 0.97
P74909 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L30 (P74909) · a predicted model of the same protein · chain 13 against A, TM-score 0.96
P80378 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S15 (P80378) · a predicted model of the same protein · chain 1o against A, TM-score 0.96
P62654 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S11 (P62654) · a predicted model of the same protein · chain 1k against A, TM-score 0.95
P0DOY7 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S17 (P0DOY7) · a predicted model of the same protein · chain 1q against A, TM-score 0.95
P62655 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S13 (P62655) · a predicted model of the same protein · chain 2m against A, TM-score 0.94
Q56435 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L24 (Q56435) · a predicted model of the same protein · chain 1Y against A, TM-score 0.94

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 Q56435
Every structure of UniProt Q72IA7
Every structure of UniProt P60493
Every structure of UniProt P60494
Every structure of UniProt Q72I12
Every structure of UniProt P74909
Every structure of UniProt Q72JR0
Every structure of UniProt P80339
Every structure of UniProt Q72GW3
Every structure of UniProt P80340
Every structure of UniProt P80374
Every structure of UniProt P80375
Every structure of UniProt P62654
Every structure of UniProt P17293
Every structure of UniProt P62655
Every structure of UniProt P24320
Every structure of UniProt P80378
Every structure of UniProt P62238
Every structure of UniProt P0DOY7
Every structure of UniProt P62659
Every structure of UniProt P62612
Elsewhere: RCSB PDB 6N9E · PDBe 6N9E · UniProt Q56435 · UniProt Q72IA7 · UniProt P60493 · UniProt P60494 · UniProt Q72I12 · UniProt P74909 · UniProt Q72JR0 · UniProt P80339 · UniProt Q72GW3 · UniProt P80340 · UniProt P80374 · UniProt P80375 · UniProt P62654 · UniProt P17293 · UniProt P62655 · UniProt P24320 · UniProt P80378 · UniProt P62238 · UniProt P0DOY7 · UniProt P62659 · UniProt P62612

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