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Crystal structure of the Thermus thermophilus 70S ribosome in complex with Hygromycin-A at 3.1A resolution

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

PDB: 5DOX
Type: protein + RNA
Length: 20,617 residues
Chains: 104
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.1
Source: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); Thermus thermophilus…
Molecule: 23S Ribosomal RNA; 5S Ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
UniProt: P60405, Q5SHN8, Q5SHN9, Q5SHQ0, Q5SHQ3, Q5SLQ1, P60488, Q5SHP8, Q5SHQ7, P60489, Q9Z9H5, Q5SHQ4, P60490, P60491, P60492, Q5SHP3, Q5SHP0, Q5SHP9, Q5SHZ1, P60493, P60494, Q5SHP6, Q5SHQ6, Q5SJE1, P80339, P35871, P80340, Q5SKU1, Q5SHR2, P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P80374, Q5SHN7, P80376, Q5SHN3, P80377, Q5SHQ1, Q5SJ76, Q5SJH3, Q5SHP7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
Ligands: HGR, SF4, MG, ZN
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · resolution 3.1 · 61 distinct chains · 29% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1A	23S Ribosomal RNA	rna	2872	—	—
1B, 2B	5S Ribosomal RNA	rna	120	—	—
1D, 2D	50S ribosomal protein L2	protein	275	10% helix, 29% strand	P60405
1E, 2E	50S ribosomal protein L3	protein	204	8% helix, 41% strand	Q5SHN8
1F, 2F	50S ribosomal protein L4	protein	202	34% helix, 14% strand	Q5SHN9
1G, 2G	50S ribosomal protein L5	protein	181	31% helix, 18% strand	Q5SHQ0
1H	50S ribosomal protein L6	protein	174	21% helix, 37% strand	Q5SHQ3
1I	50S ribosomal protein L9	protein	147	32% helix, 29% strand	Q5SLQ1
1N, 2N	50S ribosomal protein L13	protein	140	35% helix, 19% strand	P60488
1O, 2O	50S ribosomal protein L14	protein	122	8% helix, 40% strand	Q5SHP8
1P, 2P	50S ribosomal protein L15	protein	149	19% helix, 15% strand	Q5SHQ7
1Q, 2Q	50S ribosomal protein L16	protein	141	22% helix, 28% strand	P60489
1R, 2R	50S ribosomal protein L17	protein	118	54% helix, 14% strand	Q9Z9H5
1S, 2S	50S ribosomal protein L18	protein	110	45% helix, 23% strand	Q5SHQ4
1T, 2T	50S ribosomal protein L19	protein	131	26% helix, 37% strand	P60490
1U, 2U	50S ribosomal protein L20	protein	116	76% helix, 0% strand	P60491
1V, 2V	50S ribosomal protein L21	protein	101	0% helix, 61% strand	P60492
1W, 2W	50S ribosomal protein L22	protein	112	37% helix, 36% strand	Q5SHP3
1X, 2X	50S ribosomal protein L23	protein	95	21% helix, 37% strand	Q5SHP0
1Y, 2Y	50S ribosomal protein L24	protein	107	3% helix, 41% strand	Q5SHP9
1Z	50S ribosomal protein L25	protein	203	17% helix, 40% strand	Q5SHZ1
10, 20	50S ribosomal protein L27	protein	77	4% helix, 39% strand	P60493
11, 21	50S ribosomal protein L28	protein	97	30% helix, 36% strand	P60494
12, 22	50S ribosomal protein L29	protein	70	80% helix, 0% strand	Q5SHP6
13, 23	50S ribosomal protein L30	protein	59	32% helix, 29% strand	Q5SHQ6
14, 24	50S ribosomal protein L31	protein	69	0% helix, 22% strand	Q5SJE1
15, 25	50S ribosomal protein L32	protein	59	17% helix, 15% strand	P80339
16, 26	50S ribosomal protein L33	protein	53	0% helix, 57% strand	P35871
17, 27	50S ribosomal protein L34	protein	48	56% helix, 0% strand	P80340
18, 28	50S ribosomal protein L35	protein	64	31% helix, 16% strand	Q5SKU1
19, 29	50S ribosomal protein L36	protein	37	8% helix, 43% strand	Q5SHR2
1a	16S Ribosomal RNA	rna	1499	—	—
1b, 2b	30S ribosomal protein S2	protein	231	44% helix, 10% strand	P80371
1c, 2c	30S ribosomal protein S3	protein	206	33% helix, 29% strand	P80372
1d, 2d	30S ribosomal protein S4	protein	208	41% helix, 10% strand	P80373
1e, 2e	30S ribosomal protein S5	protein	148	28% helix, 41% strand	Q5SHQ5
1f, 2f	30S ribosomal protein S6	protein	100	25% helix, 47% strand	Q5SLP8
1g, 2g	30S ribosomal protein S7	protein	155	58% helix, 8% strand	P17291
1h, 2h	30S ribosomal protein S8	protein	137	23% helix, 31% strand	Q5SHQ2
1i	30S ribosomal protein S9	protein	127	24% helix, 22% strand	P80374
1j	30S ribosomal protein S10	protein	97	23% helix, 38% strand	Q5SHN7
1k, 2k	30S ribosomal protein S11	protein	114	26% helix, 27% strand	P80376
1l, 2l	30S ribosomal protein S12	protein	122	7% helix, 27% strand	Q5SHN3
1m	30S ribosomal protein S13	protein	116	41% helix, 2% strand	P80377
1n, 2n	30S ribosomal protein S14 type Z	protein	60	28% helix, 5% strand	Q5SHQ1
1o, 2o	30S ribosomal protein S15	protein	88	75% helix, 0% strand	Q5SJ76
1p, 2p	30S ribosomal protein S16	protein	82	17% helix, 34% strand	Q5SJH3
1q, 2q	30S ribosomal protein S17	protein	99	17% helix, 55% strand	Q5SHP7
1r, 2r	30S ribosomal protein S18	protein	68	46% helix, 9% strand	Q5SLQ0
1s, 2s	30S ribosomal protein S19	protein	83	16% helix, 19% strand	Q5SHP2
1t	30S ribosomal protein S20	protein	96	76% helix, 0% strand	P80380
1u, 2u	30S ribosomal protein Thx	protein	23	30% helix, 0% strand	Q5SIH3
2A	23S Ribosomal RNA	rna	2867	—	—
2H	50S ribosomal protein L6	protein	173	21% helix, 36% strand	Q5SHQ3
2I	50S ribosomal protein L9	protein	146	35% helix, 27% strand	Q5SLQ1
2Z	50S ribosomal protein L25	protein	201	15% helix, 41% strand	Q5SHZ1
2a	16S Ribosomal RNA	rna	1503	—	—
2i	30S ribosomal protein S9	protein	126	18% helix, 23% strand	P80374
2j	30S ribosomal protein S10	protein	96	21% helix, 31% strand	Q5SHN7
2m	30S ribosomal protein S13	protein	114	46% helix, 4% strand	P80377
2t	30S ribosomal protein S20	protein	98	77% helix, 0% strand	P80380

Ligands and binding sites

HGR · Hygromycin A · ligand · 2 copies · chains 1A, 2A
SF4 · Iron/sulfur cluster · ligand · 2 copies · chains 1d, 2d
MG · Magnesium ion · metal · 1718 copies · chains 1A, 19, 12, 1Q, 1F, 1Z, 1U, 1R, 11, 1P, 1N, 1E, 1X, 1W, 18, 1D, 1a, 17, 1V, 1B, 1Y, 10, 15, 1S, 1G, 1H, 1T, 13, 16, 1q, 1l, 1o, 1O, 1u, 1p, 1n, 1t, 1e, 1m, 1c, 1b, 1d, 1f, 1g, 1h, 1k, 1r, 2A, 2T, 29, 2W, 23, 25, 2E, 21, 2R, 2P, 2X, 2V, 2Q, 2D, 2U, 2N, 2F, 28, 2B, 24, 2a, 2I, 2O, 2Y, 20, 26, 2l, 2t, 2p, 2e, 2q, 2h, 2k
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	1051	0.90	0.93	126	MG
2	1002	0.90	0.92	91	MG
3	1102	0.88	0.91	87	MG
4	1152	0.88	0.91	98	MG
5	1113	0.88	0.91	83	MG

Interfaces

230 interfaces between chains.

2A–2D · 7535 Å² buried · 216 hydrogen bonds · protein-nucleic
1A–1D · 7462 Å² buried · 217 hydrogen bonds · protein-nucleic
1A–1E · 5298 Å² buried · 147 hydrogen bonds · protein-nucleic
2A–2E · 5220 Å² buried · 142 hydrogen bonds · protein-nucleic
1A–1P · 5092 Å² buried · 138 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 48 modified, 1 covalent (nucleotide modification, nonstandard, covalent ligand).

Compared structures

P60405 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P60405) · a predicted model of the same protein · chain 1D against A, TM-score 0.99
Q5SHN8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L3 (Q5SHN8) · a predicted model of the same protein · chain 1E against A, TM-score 0.99
Q5SHP8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L14 (Q5SHP8) · a predicted model of the same protein · chain 1O against A, TM-score 0.99
P60490 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L19 (P60490) · a predicted model of the same protein · chain 1T against A, TM-score 0.99
P60488 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (P60488) · a predicted model of the same protein · chain 1N against A, TM-score 0.99
Q5SHQ4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L18 (Q5SHQ4) · a predicted model of the same protein · chain 1S against A, TM-score 0.98
Q5SHQ6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L30 (Q5SHQ6) · a predicted model of the same protein · chain 13 against A, TM-score 0.98
P60492 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L21 (P60492) · a predicted model of the same protein · chain 1V against A, TM-score 0.98
Q5SHP3 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (Q5SHP3) · a predicted model of the same protein · chain 1W against A, TM-score 0.97
Q5SHQ0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L5 (Q5SHQ0) · a predicted model of the same protein · chain 1G against A, TM-score 0.97
Q5SHP6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L29 (Q5SHP6) · a predicted model of the same protein · chain 12 against A, TM-score 0.97
Q5SHP0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L23 (Q5SHP0) · a predicted model of the same protein · chain 1X against A, TM-score 0.97

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