1VY6

Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site.

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 (AA, CA)	16S Ribosomal RNA	polymer	1521	493652.2	2	GenBank (55771382)	Thermus thermophilus
2	B, EB (AB, CB)	30S ribosomal protein S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318)	Thermus thermophilus
3	C, FB (AC, CC)	30S ribosomal protein S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189)	Thermus thermophilus
4	D, GB (AD, CD)	30S ribosomal protein S4	polymer	209	24373.4	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479)	Thermus thermophilus
5	E, HB (AE, CE)	30S ribosomal protein S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719)	Thermus thermophilus
6	F, IB (AF, CF)	30S ribosomal protein S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250)	Thermus thermophilus	TS9
7	G, JB (AG, CG)	30S ribosomal protein S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177)	Thermus thermophilus
8	H, KB (AH, CH)	30S ribosomal protein S8	polymer	138	15868.6	2	UniProt (Q5SHQ2)	Thermus thermophilus
9	I, LB (AI, CI)	30S ribosomal protein S9	polymer	128	14410.6	2	UniProt (P80374) Pfam (PF00380)	Thermus thermophilus
10	J, MB (AJ, CJ)	30S ribosomal protein S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338)	Thermus thermophilus
11	K, NB (AK, CK)	30S ribosomal protein S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411)	Thermus thermophilus
12	L, OB (AL, CL)	30S ribosomal protein S12	polymer	132	14637.4	2	UniProt (Q5SHN3) Pfam (PF00164)	Thermus thermophilus
13	M, PB (AM, CM)	30S ribosomal protein S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416)	Thermus thermophilus
14	N, QB (AN, CN)	30S ribosomal protein S14 type Z	polymer	61	7158.7	2	UniProt (Q5SHQ1)	Thermus thermophilus
15	O, RB (AO, CO)	30S ribosomal protein S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312)	Thermus thermophilus
16	P, SB (AP, CP)	30S ribosomal protein S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886)	Thermus thermophilus
17	Q, TB (AQ, CQ)	30S ribosomal protein S17	polymer	105	12325.7	2	UniProt (Q5SHP7)	Thermus thermophilus
18	R, UB (AR, CR)	30S ribosomal protein S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084)	Thermus thermophilus
19	S, VB (AS, CS)	30S ribosomal protein S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203)	Thermus thermophilus
20	T, WB (AT, CT)	30S ribosomal protein S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649)	Thermus thermophilus
21	U, XB (AU, CU)	30S ribosomal protein Thx	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070)	Thermus thermophilus	S31
22	V, YB (AV, CV)	mRNA	polymer	24	7804.7	2		Synthetic
23	W, ZB (AW, CW)	Cytidine-Puromycin	polymer	2	793.7	2		Synthetic
24	AC, X (AX, CX)	P-site tRNA	polymer	77	25005.1	2		Escherichia coli
25	BC, Y (BA, DA)	23S Ribosomal RNA	polymer	2915	947895.4	2	GenBank (55771382)	Thermus thermophilus
26	CC, Z (BB, DB)	5S Ribosomal RNA	polymer	121	39188.4	2	GenBank (55771382)	Thermus thermophilus
27	AA, DC (BD, DD)	50S ribosomal protein L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947)	Thermus thermophilus
28	BA, EC (BE, DE)	50S ribosomal protein L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297)	Thermus thermophilus
29	CA, FC (BF, DF)	50S ribosomal protein L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573)	Thermus thermophilus	L1e
30	DA, GC (BG, DG)	50S ribosomal protein L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673)	Thermus thermophilus
31	EA, HC (BH, DH)	50S ribosomal protein L6	polymer	180	19568.9	2	UniProt (Q5SHQ3)	Thermus thermophilus
32	FA, IC (BI, DI)	50S ribosomal protein L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948)	Thermus thermophilus
33	GA, JC (BN, DN)	50S ribosomal protein L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572)	Thermus thermophilus
34	HA, KC (BO, DO)	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238)	Thermus thermophilus
35	IA, LC (BP, DP)	50S ribosomal protein L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828)	Thermus thermophilus
36	JA, MC (BQ, DQ)	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252)	Thermus thermophilus
37	KA, NC (BR, DR)	50S ribosomal protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196)	Thermus thermophilus
38	LA, OC (BS, DS)	50S ribosomal protein L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861)	Thermus thermophilus	TL24
39	MA, PC (BT, DT)	50S ribosomal protein L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245)	Thermus thermophilus
40	NA, QC (BU, DU)	50S ribosomal protein L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453)	Thermus thermophilus
41	OA, RC (BV, DV)	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829)	Thermus thermophilus
42	PA, SC (BW, DW)	50S ribosomal protein L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237)	Thermus thermophilus
43	QA, TC (BX, DX)	50S ribosomal protein L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276)	Thermus thermophilus
44	RA, UC (BY, DY)	50S ribosomal protein L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136)	Thermus thermophilus
45	SA, VC (BZ, DZ)	50S ribosomal protein L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693)	Thermus thermophilus	TL5
46	TA, WC (B0, D0)	50S ribosomal protein L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016)	Thermus thermophilus
47	UA, XC (B1, D1)	50S ribosomal protein L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830)	Thermus thermophilus
48	VA, YC (B2, D2)	50S ribosomal protein L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831)	Thermus thermophilus
49	WA, ZC (B3, D3)	50S ribosomal protein L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327)	Thermus thermophilus
50	AD, XA (B4, D4)	50S ribosomal protein L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197)	Thermus thermophilus
51	BD, YA (B5, D5)	50S ribosomal protein L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783)	Thermus thermophilus
52	CD, ZA (B6, D6)	50S ribosomal protein L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471)	Thermus thermophilus
53	AB, DD (B7, D7)	50S ribosomal protein L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468)	Thermus thermophilus
54	BB, ED (B8, D8)	50S ribosomal protein L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632)	Thermus thermophilus
55	CB, FD (B9, D9)	50S ribosomal protein L36	polymer	37	4435.4	2	UniProt (Q5SHR2) Pfam (PF00444)	Thermus thermophilus	Ribosomal protein B
56	AAA, AAB, ABA, ABB, ACA... (BA, DA, AA, AX, BD...)	MAGNESIUM ION	non-polymer		24.3	1764	Chemie (MG)
57	LK, PUA (AD, CD)	IRON/SULFUR CLUSTER	non-polymer		351.6	2	Chemie (SF4)
58	EOA, GOA, GTB, JOA, KTB... (B4, B5, DY, B6, D4...)	ZINC ION	non-polymer		65.4	12	Chemie (ZN)
59	VK, YUA (AX, DA)	POTASSIUM ION	non-polymer		39.1	2	Chemie (K)
60	AUB, AVB, BUB, BVB, CUB... (BB, CJ, BD, CL, BE...)	water	water		18.0	2071	Chemie (HOH)

Contents of the asymmetric unit

Polymers	Number of chains	110
	Total formula weight	4403398.4
Non-Polymers*	Number of molecules	1780
	Total formula weight	44440.4
All*	Total formula weight	4447838.8

*Water molecules are not included.