12DQ

Crystal structure of Thermus thermophilus 70S ribosome in complex with sparsomycin, protein Y, and P-site MTI-tripeptidyl-tRNA analog ACCA-ITM at 2.75A resolution

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, DB (1A, 2A)	23S Ribosomal RNA	polymer	2915	948007.6	2	GenBank (55771382)	Thermus thermophilus HB8
2	B, EB (1B, 2B)	5S Ribosomal RNA	polymer	121	39188.4	2	GenBank (AP008226.1)	Thermus thermophilus HB8
3	C, FB (1D, 2D)	50S ribosomal protein L2	polymer	276	30532.6	2	UniProt (P60405)	Thermus thermophilus HB8
4	D, GB (1E, 2E)	50S ribosomal protein L3	polymer	206	22450.2	2	UniProt (Q5SHN8)	Thermus thermophilus HB8
5	E, HB (1F, 2F)	50S ribosomal protein L4	polymer	210	23271.9	2	UniProt (Q5SHN9)	Thermus thermophilus HB8	L1e
6	F, IB (1G, 2G)	50S ribosomal protein L5	polymer	182	21061.6	2	UniProt (Q5SHQ0)	Thermus thermophilus HB8
7	G, JB (1H, 2H)	50S ribosomal protein L6	polymer	180	19568.9	2	UniProt (P0DOY8)	Thermus thermophilus HB8
8	H, KB (1I, 2I)	50S ribosomal protein L9	polymer	148	16422.2	2	UniProt (Q5SLQ1)	Thermus thermophilus HB8
9	I, LB (1N, 2N)	50S ribosomal protein L13	polymer	140	15927.9	2	UniProt (P60488)	Thermus thermophilus HB8
10	J, MB (1O, 2O)	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8)	Thermus thermophilus HB8
11	K, NB (1P, 2P)	50S ribosomal protein L15	polymer	150	16319.1	2	UniProt (Q5SHQ7)	Thermus thermophilus HB8
12	L, OB (1Q, 2Q)	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489)	Thermus thermophilus HB8
13	M, PB (1R, 2R)	50S ribosomal protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5)	Thermus thermophilus HB8
14	N, QB (1S, 2S)	50S ribosomal protein L18	polymer	112	12639.8	2	UniProt (Q5SHQ4)	Thermus thermophilus HB8	TL24
15	O, RB (1T, 2T)	50S ribosomal protein L19	polymer	146	17188.8	2	UniProt (P60490)	Thermus thermophilus HB8
16	P, SB (1U, 2U)	50S ribosomal protein L20	polymer	118	13779.3	2	UniProt (P60491)	Thermus thermophilus HB8
17	Q, TB (1V, 2V)	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492)	Thermus thermophilus HB8
18	R, UB (1W, 2W)	50S ribosomal protein L22	polymer	113	12808.1	2	UniProt (Q5SHP3)	Thermus thermophilus HB8
19	S, VB (1X, 2X)	50S ribosomal protein L23	polymer	96	10759.8	2	UniProt (Q5SHP0)	Thermus thermophilus HB8
20	T, WB (1Y, 2Y)	50S ribosomal protein L24	polymer	110	12085.6	2	UniProt (Q5SHP9)	Thermus thermophilus HB8
21	U, XB (1Z, 2Z)	50S ribosomal protein L25	polymer	206	23238.6	2	UniProt (Q5SHZ1)	Thermus thermophilus HB8	TL5
22	V, YB (10, 20)	50S ribosomal protein L27	polymer	85	9529.1	2	UniProt (P60493)	Thermus thermophilus HB8
23	W, ZB (11, 21)	50S ribosomal protein L28	polymer	98	11004.2	2	UniProt (P60494)	Thermus thermophilus HB8
24	AC, X (12, 22)	50S ribosomal protein L29	polymer	72	8670.3	2	UniProt (Q5SHP6)	Thermus thermophilus HB8
25	BC, Y (13, 23)	50S ribosomal protein L30	polymer	60	6799.1	2	UniProt (Q5SHQ6)	Thermus thermophilus HB8
26	CC, Z (14, 24)	50S ribosomal protein L31	polymer	71	8300.5	2	UniProt (Q5SJE1)	Thermus thermophilus HB8
27	AA, DC (15, 25)	50S ribosomal protein L32	polymer	60	6722.1	2	UniProt (P80339)	Thermus thermophilus HB8
28	BA, EC (16, 26)	50S ribosomal protein L33	polymer	54	6632.9	2	UniProt (P35871)	Thermus thermophilus HB8
29	CA, FC (17, 27)	50S ribosomal protein L34	polymer	49	6132.4	2	UniProt (P80340)	Thermus thermophilus HB8
30	DA, GC (18, 28)	50S ribosomal protein L35	polymer	65	7506.2	2	UniProt (Q5SKU1)	Thermus thermophilus HB8
31	EA, HC (19, 29)	50S ribosomal protein L36	polymer	37	4435.4	2	UniProt (Q5SHR2)	Thermus thermophilus HB8	Ribosomal protein B
32	FA, IC (1a, 2a)	16S Ribosomal RNA	polymer	1521	493863.6	2	GenBank (55771382)	Thermus thermophilus HB8
33	GA, JC (1b, 2b)	30S ribosomal protein S2	polymer	256	29317.7	2	UniProt (P80371)	Thermus thermophilus HB8
34	HA, KC (1c, 2c)	30S ribosomal protein S3	polymer	239	26751.1	2	UniProt (P80372)	Thermus thermophilus HB8
35	IA, LC (1d, 2d)	30S ribosomal protein S4	polymer	209	24373.4	2	UniProt (P80373)	Thermus thermophilus HB8
36	JA, MC (1e, 2e)	30S ribosomal protein S5	polymer	162	17583.4	2	UniProt (Q5SHQ5)	Thermus thermophilus HB8
37	KA, NC (1f, 2f)	30S ribosomal protein S6	polymer	101	11988.8	2	UniProt (Q5SLP8)	Thermus thermophilus HB8	TS9
38	LA, OC (1g, 2g)	30S ribosomal protein S7	polymer	156	18051.0	2	UniProt (P17291)	Thermus thermophilus HB8
39	MA, PC (1h, 2h)	30S ribosomal protein S8	polymer	138	15868.6	2	UniProt (P0DOY9)	Thermus thermophilus HB8
40	NA, QC (1i, 2i)	30S ribosomal protein S9	polymer	128	14410.6	2	UniProt (P80374)	Thermus thermophilus HB8
41	OA, RC (1j, 2j)	30S ribosomal protein S10	polymer	105	11955.0	2	UniProt (Q5SHN7)	Thermus thermophilus HB8
42	PA, SC (1k, 2k)	30S ribosomal protein S11	polymer	129	13737.9	2	UniProt (P80376)	Thermus thermophilus HB8
43	QA, TC (1l, 2l)	30S ribosomal protein S12	polymer	132	14683.5	2	UniProt (Q5SHN3)	Thermus thermophilus HB8
44	RA, UC (1m, 2m)	30S ribosomal protein S13	polymer	126	14338.9	2	UniProt (P80377)	Thermus thermophilus HB8
45	SA, VC (1n, 2n)	30S ribosomal protein S14 type Z	polymer	61	7158.7	2	UniProt (P0DOY6)	Thermus thermophilus HB8
46	TA, WC (1o, 2o)	30S ribosomal protein S15	polymer	89	10578.4	2	UniProt (Q5SJ76)	Thermus thermophilus HB8
47	UA, XC (1p, 2p)	30S ribosomal protein S16	polymer	88	10410.0	2	UniProt (Q5SJH3)	Thermus thermophilus HB8
48	VA, YC (1q, 2q)	30S ribosomal protein S17	polymer	105	12325.7	2	UniProt (P0DOY7)	Thermus thermophilus HB8
49	WA, ZC (1r, 2r)	30S ribosomal protein S18	polymer	88	10258.3	2	UniProt (Q5SLQ0)	Thermus thermophilus HB8
50	AD, XA (1s, 2s)	30S ribosomal protein S19	polymer	93	10605.5	2	UniProt (Q5SHP2)	Thermus thermophilus HB8
51	BD, YA (1t, 2t)	30S ribosomal protein S20	polymer	106	11736.1	2	UniProt (P80380)	Thermus thermophilus HB8
52	CD, ZA (1u, 2u)	30S ribosomal protein Thx	polymer	27	3350.0	2	UniProt (Q5SIH3)	Thermus thermophilus HB8	S31
53	AB, DD (1y, 2y)	Ribosome-associated inhibitor A	polymer	113	12803.6	2	UniProt (P0AD49)	Escherichia coli K-12	Protein Y,pY,Ribosome associated factor Y,Spot Y
54	BB, ED (1x, 2x)	P-site Peptidyl-tRNA Analog RNA	polymer	4	1222.8	2		Escherichia coli
55	CB, FD (1v, 2v)	P-site Peptidyl-tRNA Analog Peptide	polymer	3	363.5	2		Escherichia coli
56	AAA, AAB, AAC, ABA, ABB... (1A, 1a, 2A, 1i, 2B...)	MAGNESIUM ION	non-polymer		24.3	2495	Chemie (MG) PubChem (888)
57	AWC, OQA (2x, 1A)	SPARSOMYCIN	non-polymer		361.4	2	Chemie (SPS)
58	PQA, UKC, VKC, WKC (1A, 2A)	(4S)-2-METHYL-2,4-PENTANEDIOL	non-polymer		118.2	4	Chemie (MPD) PubChem (5288834)
59	TRA (1B)	ARGININE	non-polymer		175.2	1	Chemie (ARG)
60	AWA, BOC, DOC, HOC, HVA... (14, 25, 26, 29, 1Y...)	ZINC ION	non-polymer		65.4	12	Chemie (ZN) PubChem (32051)
61	VWA (18)	(4R)-2-METHYLPENTANE-2,4-DIOL	non-polymer		118.2	1	Chemie (MRD) PubChem (5288845)
62	NVC, THB (2d, 1d)	IRON/SULFUR CLUSTER	non-polymer		351.6	2	Chemie (SF4)
63	AXC, AYC, AZC, BWC, BXC... (14, 2H, 2f, 1A, 15...)	water	water		18.0	8292	Chemie (HOH)

Contents of the asymmetric unit

Polymers	Number of chains	110
	Total formula weight	4365710.5
Non-Polymers*	Number of molecules	2517
	Total formula weight	63618.1
All*	Total formula weight	4429328.6

*Water molecules are not included.