1VY5

Crystal structure of the Thermus thermophilus 70S ribosome in the post-catalysis state of peptide bond formation containing dipeptydil-tRNA in the A site and deacylated 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	AA, CA	16S Ribosomal RNA	polymer	1521	493652.2	2	GenBank (55771382)	Thermus thermophilus HB8
2	AB, CB	30S ribosomal protein S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
3	AC, CC	30S ribosomal protein S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
4	AD, CD	30S ribosomal protein S4	polymer	209	24373.4	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
5	AE, CE	30S ribosomal protein S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
6	AF, CF	30S ribosomal protein S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	TS9
7	AG, CG	30S ribosomal protein S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
8	AH, CH	30S ribosomal protein S8	polymer	138	15868.6	2	UniProt (P0DOY9) Pfam (PF00410) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
9	AI, CI	30S ribosomal protein S9	polymer	128	14410.6	2	UniProt (P80374) Pfam (PF00380) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
10	AJ, CJ	30S ribosomal protein S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
11	AK, CK	30S ribosomal protein S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
12	AL, CL	30S ribosomal protein S12	polymer	132	14637.4	2	UniProt (Q5SHN3) Pfam (PF00164) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
13	AM, CM	30S ribosomal protein S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
14	AN, CN	30S ribosomal protein S14 type Z	polymer	61	7158.7	2	UniProt (P0DOY6) Pfam (PF00253) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
15	AO, CO	30S ribosomal protein S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
16	AP, CP	30S ribosomal protein S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
17	AQ, CQ	30S ribosomal protein S17	polymer	105	12325.7	2	UniProt (P0DOY7) Pfam (PF00366) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
18	AR, CR	30S ribosomal protein S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
19	AS, CS	30S ribosomal protein S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
20	AT, CT	30S ribosomal protein S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
21	AU, CU	30S ribosomal protein Thx	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	S31
22	AV, CV	mRNA	polymer	24	7804.7	2		Synthetic DNA
23	AW, CW	A-site tRNA	polymer	76	24923.3	2		Escherichia coli
24	AX, CX	P-site tRNA	polymer	77	24846.9	2		Escherichia coli
25	AY, CY	E-site tRNA	polymer	76	24645.9	2		Escherichia coli
26	BA, DA	23S Ribosomal RNA	polymer	2915	947895.4	2	GenBank (55771382)	Thermus thermophilus HB8
27	BB, DB	5S Ribosomal RNA	polymer	121	39188.4	2	GenBank (55771382)	Thermus thermophilus HB8
28	BD, DD	50S ribosomal protein L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
29	BE, DE	50S ribosomal protein L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
30	BF, DF	50S ribosomal protein L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	L1e
31	BG, DG	50S ribosomal protein L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
32	BH, DH	50S ribosomal protein L6	polymer	180	19568.9	2	UniProt (P0DOY8) Pfam (PF00347) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
33	BI, DI	50S ribosomal protein L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
34	BN, DN	50S ribosomal protein L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
35	BO, DO	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
36	BP, DP	50S ribosomal protein L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
37	BQ, DQ	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
38	BR, DR	50S ribosomal protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
39	BS, DS	50S ribosomal protein L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	TL24
40	BT, DT	50S ribosomal protein L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
41	BU, DU	50S ribosomal protein L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
42	BV, DV	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
43	BW, DW	50S ribosomal protein L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
44	BX, DX	50S ribosomal protein L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
45	BY, DY	50S ribosomal protein L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
46	BZ, DZ	50S ribosomal protein L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	TL5
47	B0, D0	50S ribosomal protein L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
48	B1, D1	50S ribosomal protein L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
49	B2, D2	50S ribosomal protein L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
50	B3, D3	50S ribosomal protein L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
51	B4, D4	50S ribosomal protein L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
52	B5, D5	50S ribosomal protein L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
53	B6, D6	50S ribosomal protein L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
54	B7, D7	50S ribosomal protein L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
55	B8, D8	50S ribosomal protein L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
56	B9, D9	50S ribosomal protein L36	polymer	37	4435.4	2	UniProt (Q5SHR2) Pfam (PF00444) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Ribosomal protein B
57	BA, CA, DA, AA, DB...	MAGNESIUM ION	non-polymer		24.3	2077	Chemie (MG)
58	CD, AD	IRON/SULFUR CLUSTER	non-polymer		351.6	2	Chemie (SF4)
59	B6, CN, B9, DY, BY...	ZINC ION	non-polymer		65.4	12	Chemie (ZN)
60	AX, CX	POTASSIUM ION	non-polymer		39.1	2	Chemie (K)
61		water	water		18.0	3062	Chemie (HOH)

Contents of the asymmetric unit

Polymers	Number of chains	112
	Total formula weight	4500632.8
Non-Polymers*	Number of molecules	2093
	Total formula weight	52047.9
All*	Total formula weight	4552680.7

*Water molecules are not included.