4V5D

Structure of the Thermus thermophilus 70S ribosome in complex with mRNA, paromomycin, acylated A- and P-site tRNAs, and E-site tRNA.

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, FB (AA, CA)	16S ribosomal RNA	polymer	1522	493958.3	2		THERMUS THERMOPHILUS
2	B, GB (AB, CB)	30S RIBOSOMAL PROTEIN S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318)	THERMUS THERMOPHILUS
3	C, HB (AC, CC)	30S RIBOSOMAL PROTEIN S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189)	THERMUS THERMOPHILUS
4	D, IB (AD, CD)	30S RIBOSOMAL PROTEIN S4	polymer	209	24373.4	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479)	THERMUS THERMOPHILUS
5	E, JB (AE, CE)	30S RIBOSOMAL PROTEIN S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719)	THERMUS THERMOPHILUS
6	F, KB (AF, CF)	30S RIBOSOMAL PROTEIN S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250)	THERMUS THERMOPHILUS	TS9
7	G, LB (AG, CG)	30S RIBOSOMAL PROTEIN S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177)	THERMUS THERMOPHILUS
8	H, MB (AH, CH)	30S RIBOSOMAL PROTEIN S8	polymer	138	15868.6	2	UniProt (Q5SHQ2)	THERMUS THERMOPHILUS
9	I, NB (AI, CI)	30S RIBOSOMAL PROTEIN S9	polymer	128	14429.7	2	UniProt (P62669) Pfam (PF00380)	THERMUS THERMOPHILUS
10	J, OB (AJ, CJ)	30S RIBOSOMAL PROTEIN S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338)	THERMUS THERMOPHILUS
11	K, PB (AK, CK)	30S RIBOSOMAL PROTEIN S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411)	THERMUS THERMOPHILUS
12	L, QB (AL, CL)	30S RIBOSOMAL PROTEIN S12	polymer	135	14920.8	2	UniProt (Q5SHN3) Pfam (PF00164)	THERMUS THERMOPHILUS
13	M, RB (AM, CM)	30S RIBOSOMAL PROTEIN S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416)	THERMUS THERMOPHILUS
14	N, SB (AN, CN)	30S RIBOSOMAL PROTEIN S14	polymer	61	7158.7	2	UniProt (Q5SHQ1)	THERMUS THERMOPHILUS
15	O, TB (AO, CO)	30S RIBOSOMAL PROTEIN S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312)	THERMUS THERMOPHILUS
16	P, UB (AP, CP)	30S RIBOSOMAL PROTEIN S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886)	THERMUS THERMOPHILUS
17	Q, VB (AQ, CQ)	30S RIBOSOMAL PROTEIN S17	polymer	105	12325.7	2	UniProt (Q5SHP7)	THERMUS THERMOPHILUS
18	R, WB (AR, CR)	30S RIBOSOMAL PROTEIN S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084)	THERMUS THERMOPHILUS
19	S, XB (AS, CS)	30S RIBOSOMAL PROTEIN S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203)	THERMUS THERMOPHILUS
20	T, YB (AT, CT)	30S RIBOSOMAL PROTEIN S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649)	THERMUS THERMOPHILUS
21	U, ZB (AU, CU)	30S RIBOSOMAL PROTEIN THX	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070)	THERMUS THERMOPHILUS
22	AC, DC, V, Y (AV, AY, CV, CY)	P AND A-SITE PHE-TRNA PHE	polymer	77	24615.7	4		ESCHERICHIA COLI
23	BC, W (AW, CW)	E-SITE TRNA PHE	polymer	76	24485.5	2		ESCHERICHIA COLI
24	CC, X (AX, CX)	MRNA	polymer	11	3436.1	2		synthetic construct
25	EC, Z (B0, D0)	50S RIBOSOMAL PROTEIN L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016)	THERMUS THERMOPHILUS
26	AA, FC (B1, D1)	50S RIBOSOMAL PROTEIN L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830)	THERMUS THERMOPHILUS
27	BA, GC (B2, D2)	50S RIBOSOMAL PROTEIN L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831)	THERMUS THERMOPHILUS
28	CA, HC (B3, D3)	50S RIBOSOMAL PROTEIN L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327)	THERMUS THERMOPHILUS
29	DA, IC (B4, D4)	50S RIBOSOMAL PROTEIN L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197)	THERMUS THERMOPHILUS
30	EA, JC (B5, D5)	50S RIBOSOMAL PROTEIN L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783)	THERMUS THERMOPHILUS
31	FA, KC (B6, D6)	50S RIBOSOMAL PROTEIN L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471)	THERMUS THERMOPHILUS
32	GA, LC (B7, D7)	50S RIBOSOMAL PROTEIN L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468)	THERMUS THERMOPHILUS
33	HA, MC (B8, D8)	50S RIBOSOMAL PROTEIN L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632)	THERMUS THERMOPHILUS
34	IA, NC (B9, D9)	50S RIBOSOMAL PROTEIN L36	polymer	37	4435.4	2	UniProt (Q5SHR2) Pfam (PF00444)	THERMUS THERMOPHILUS
35	JA, OC (BA, DA)	23S RIBOSOMAL RNA	polymer	2822	917797.0	2		THERMUS THERMOPHILUS
36	KA, PC (BB, DB)	5S RIBOSOMAL RNA	polymer	122	39494.5	2		THERMUS THERMOPHILUS
37	LA, QC (BC, DC)	50S RIBOSOMAL PROTEIN L1	polymer	229	24872.7	2	UniProt (Q5SLP7) Pfam (PF00687)	THERMUS THERMOPHILUS
38	MA, RC (BD, DD)	50S RIBOSOMAL PROTEIN L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947)	THERMUS THERMOPHILUS
39	NA, SC (BE, DE)	50S RIBOSOMAL PROTEIN L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297)	THERMUS THERMOPHILUS
40	OA, TC (BF, DF)	50S RIBOSOMAL PROTEIN L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573)	THERMUS THERMOPHILUS
41	PA, UC (BG, DG)	50S RIBOSOMAL PROTEIN L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673)	THERMUS THERMOPHILUS
42	QA, VC (BH, DH)	50S RIBOSOMAL PROTEIN L6	polymer	180	19568.9	2	UniProt (Q5SHQ3)	THERMUS THERMOPHILUS
43	RA, WC (BI, DI)	50S RIBOSOMAL PROTEIN L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948)	THERMUS THERMOPHILUS
44	SA, XC (BN, DN)	50S RIBOSOMAL PROTEIN L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572)	THERMUS THERMOPHILUS
45	TA, YC (BO, DO)	50S RIBOSOMAL PROTEIN L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238)	THERMUS THERMOPHILUS
46	UA, ZC (BP, DP)	50S RIBOSOMAL PROTEIN L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828)	THERMUS THERMOPHILUS
47	AD, VA (BQ, DQ)	50S RIBOSOMAL PROTEIN L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252)	THERMUS THERMOPHILUS
48	BD, WA (BR, DR)	50S RIBOSOMAL PROTEIN L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196)	THERMUS THERMOPHILUS
49	CD, XA (BS, DS)	50S RIBOSOMAL PROTEIN L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861)	THERMUS THERMOPHILUS
50	DD, YA (BT, DT)	50S RIBOSOMAL PROTEIN L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245)	THERMUS THERMOPHILUS
51	ED, ZA (BU, DU)	50S RIBOSOMAL PROTEIN L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453)	THERMUS THERMOPHILUS
52	AB, FD (BV, DV)	50S RIBOSOMAL PROTEIN L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829)	THERMUS THERMOPHILUS
53	BB, GD (BW, DW)	50S RIBOSOMAL PROTEIN L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237)	THERMUS THERMOPHILUS
54	CB, HD (BX, DX)	50S RIBOSOMAL PROTEIN L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276)	THERMUS THERMOPHILUS
55	DB, ID (BY, DY)	50S RIBOSOMAL PROTEIN L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136)	THERMUS THERMOPHILUS
56	EB, JD (BZ, DZ)	50S RIBOSOMAL PROTEIN L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693)	THERMUS THERMOPHILUS
57	AAA, AAB, ABA, ABB, ACA... (BA, DA, BB, DD, AA...)	MAGNESIUM ION	non-polymer		24.3	1346	Chemie (MG)
58	AL, CLA (AA, CA)	PAROMOMYCIN	non-polymer		615.6	2	Chemie (PAR)
59	CL, DLA, GM, GMA, ILA... (AD, CD, B9, D9, CN...)	ZINC ION	non-polymer		65.4	6	Chemie (ZN)

Sequence modifications

AL, CL: 1 - 4 (PDB: 4V5D)
AL, CL: 5 - 135 (UniProt: Q5SHN3)

Contents of the asymmetric unit

Polymers	Number of chains	114
	Total formula weight	4481875.6
Non-Polymers*	Number of molecules	1354
	Total formula weight	34338.2
All*	Total formula weight	4516213.8

*Water molecules are not included.