4W2I

Crystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sites

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
2	AB, CB	30S Ribosomal Protein S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318) In PDB	Thermus thermophilus
3	AC, CC	30S Ribosomal Protein S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189) In PDB	Thermus thermophilus
4	AD, CD	30S Ribosomal Protein S4	polymer	209	24373.4	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479) In PDB	Thermus thermophilus
5	AE, CE	30S Ribosomal Protein S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719) In PDB	Thermus thermophilus
6	AF, CF	30S Ribosomal Protein S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250) In PDB	Thermus thermophilus
7	AG, CG	30S Ribosomal Protein S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177) In PDB	Thermus thermophilus
8	AH, CH	30S Ribosomal Protein S8	polymer	138	15868.6	2	UniProt (Q5SHQ2) In PDB	Thermus thermophilus
9	AI, CI	30S Ribosomal Protein S9	polymer	128	14410.6	2	UniProt (P80374) Pfam (PF00380) In PDB	Thermus thermophilus
10	AJ, CJ	30S Ribosomal Protein S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338) In PDB	Thermus thermophilus
11	AK, CK	30S Ribosomal Protein S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411) In PDB	Thermus thermophilus
12	AL, CL	30S Ribosomal Protein S12	polymer	132	14637.4	2	UniProt (Q5SHN3) Pfam (PF00164) In PDB	Thermus thermophilus
13	AM, CM	30S Ribosomal Protein S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416) In PDB	Thermus thermophilus
14	AN, CN	30S Ribosomal Protein S14	polymer	61	7158.7	2	UniProt (Q5SHQ1) In PDB	Thermus thermophilus
15	AO, CO	30S Ribosomal Protein S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312) In PDB	Thermus thermophilus
16	AP, CP	30S Ribosomal Protein S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886) In PDB	Thermus thermophilus
17	AQ, CQ	30S Ribosomal Protein S17	polymer	105	12325.7	2	UniProt (Q5SHP7) In PDB	Thermus thermophilus
18	AR, CR	30S Ribosomal Protein S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084) In PDB	Thermus thermophilus
19	AS, CS	30S Ribosomal Protein S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203) In PDB	Thermus thermophilus
20	AT, CT	30S Ribosomal Protein S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649) In PDB	Thermus thermophilus
21	AU, CU	30S Ribosomal Protein THX	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070) In PDB	Thermus thermophilus
22	AV, CV	mRNA	polymer	24	7804.7	2		synthetic construct
23	AW, AY, CW, CY	A/P-site tRNA	polymer	76	24645.9	4		Escherichia coli
24	AX, CX	E-site tRNA	polymer	77	24846.9	2		Escherichia coli
25	BA, DA	23S Ribosomal RNA	polymer	2915	947895.4	2	GenBank (55771382)	Thermus thermophilus
26	BB, DB	5S Ribosomal RNA	polymer	121	39188.4	2	GenBank (55771382)	Thermus thermophilus
27	BD, DD	50S Ribosomal Protein L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947) In PDB	Thermus thermophilus
28	BE, DE	50S Ribosomal Protein L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297) In PDB	Thermus thermophilus
29	BF, DF	50S Ribosomal Protein L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573) In PDB	Thermus thermophilus
30	BG, DG	50S Ribosomal Protein L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673) In PDB	Thermus thermophilus
31	BH, DH	50S Ribosomal Protein L6	polymer	180	19568.9	2	UniProt (Q5SHQ3) In PDB	Thermus thermophilus
32	BI, DI	50S Ribosomal Protein L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948) In PDB	Thermus thermophilus
33	BN, DN	50S Ribosomal Protein L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572) In PDB	Thermus thermophilus
34	BO, DO	50S Ribosomal Protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238) In PDB	Thermus thermophilus
35	BP, DP	50S Ribosomal Protein L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828) In PDB	Thermus thermophilus
36	BQ, DQ	50S Ribosomal Protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252) In PDB	Thermus thermophilus
37	BR, DR	50S Ribosomal Protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196) In PDB	Thermus thermophilus
38	BS, DS	50S Ribosomal Protein L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861) In PDB	Thermus thermophilus
39	BT, DT	50S Ribosomal Protein L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245) In PDB	Thermus thermophilus
40	BU, DU	50S Ribosomal Protein L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453) In PDB	Thermus thermophilus
41	BV, DV	50S Ribosomal Protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829) In PDB	Thermus thermophilus
42	BW, DW	50S Ribosomal Protein L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237) In PDB	Thermus thermophilus
43	BX, DX	50S Ribosomal Protein L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276) In PDB	Thermus thermophilus
44	BY, DY	50S Ribosomal Protein L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136) In PDB	Thermus thermophilus
45	BZ, DZ	50S Ribosomal Protein L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693) In PDB	Thermus thermophilus
46	B0, D0	50S Ribosomal Protein L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016) In PDB	Thermus thermophilus
47	B1, D1	50S Ribosomal Protein L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830) In PDB	Thermus thermophilus
48	B2, D2	50S Ribosomal Protein L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831) In PDB	Thermus thermophilus
49	B3, D3	50S Ribosomal Protein L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327) In PDB	Thermus thermophilus
50	B4, D4	50S Ribosomal Protein L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197) In PDB	Thermus thermophilus
51	B5, D5	50S Ribosomal Protein L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783) In PDB	Thermus thermophilus
52	B6, D6	50S Ribosomal Protein L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471) In PDB	Thermus thermophilus
53	B7, D7	50S Ribosomal Protein L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468) In PDB	Thermus thermophilus
54	B8, D8	50S Ribosomal Protein L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632) In PDB	Thermus thermophilus
55	B9, D9	50S Ribosomal Protein L36	polymer	37	4435.4	2	UniProt (Q5SHR2) Pfam (PF00444) In PDB	Thermus thermophilus
56	BA, CA, DA, DB, CD...	MAGNESIUM ION	non-polymer		24.3	2013	Chemie (MG)
57	AX, CW, CA, AA, CX...	NEGAMYCIN	non-polymer		248.3	19	Chemie (NEG)
58	CD, AD	IRON/SULFUR CLUSTER	non-polymer		351.6	2	Chemie (SF4)
59	B9, D9, BY, AN, CN...	ZINC ION	non-polymer		65.4	12	Chemie (ZN)
60	CX, AX	POTASSIUM ION	non-polymer		39.1	2	Chemie (K)
61		water	water		18.0	3049	Chemie (HOH)

Contents of the asymmetric unit

Polymers	Number of chains	112
	Total formula weight	4500078.1
Non-Polymers*	Number of molecules	2048
	Total formula weight	55209.7
All*	Total formula weight	4555287.7

*Water molecules are not included.