4V8F

Crystal structure analysis of ribosomal decoding (near-cognate tRNA-ttyr complex with paromomycin).

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, CC (AA, DA)	RNA (2912-MER)	polymer	2912	947013.0	2	GenBank (AP008226.1)	Thermus thermophilus
2	B, DC (AB, DB)	5S RIBOSOMAL RNA	polymer	122	39540.6	2	GenBank (AP008226.1)	Thermus thermophilus
3	C, EC (AD, DD)	50S ribosomal protein L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947)	Thermus thermophilus
4	D, FC (AE, DE)	50S ribosomal protein L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297)	Thermus thermophilus
5	E, GC (AF, DF)	50S ribosomal protein L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573)	Thermus thermophilus
6	F, HC (AG, DG)	50S ribosomal protein L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673)	Thermus thermophilus
7	G, IC (AH, DH)	50S ribosomal protein L6	polymer	180	19568.9	2	UniProt (Q5SHQ3)	Thermus thermophilus
8	H, JC (AK, DK)	50S ribosomal protein L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948)	Thermus thermophilus
9	I, KC (AM, DM)	50S ribosomal protein L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572)	Thermus thermophilus
10	J, LC (AN, DN)	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238)	Thermus thermophilus
11	K, MC (AO, DO)	50S ribosomal protein L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828)	Thermus thermophilus
12	L, NC (AP, DP)	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252)	Thermus thermophilus
13	M, OC (A0, D0)	50S ribosomal protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196)	Thermus thermophilus
14	N, PC (AQ, DQ)	50S ribosomal protein L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861)	Thermus thermophilus
15	O, QC (AR, DR)	50S ribosomal protein L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245)	Thermus thermophilus
16	P, RC (A1, D1)	50S ribosomal protein L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453)	Thermus thermophilus
17	Q, SC (A2, D2)	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829)	Thermus thermophilus
18	R, TC (AS, DS)	50S ribosomal protein L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237)	Thermus thermophilus
19	S, UC (AT, DT)	50S ribosomal protein L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276)	Thermus thermophilus
20	T, VC (AU, DU)	50S ribosomal protein L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136)	Thermus thermophilus
21	U, WC (AV, DV)	50S ribosomal protein L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693)	Thermus thermophilus
22	V, XC (A3, D3)	50S ribosomal protein L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016)	Thermus thermophilus
23	W, YC (AZ, DZ)	50S ribosomal protein L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830)	Thermus thermophilus
24	X, ZC (AW, DW)	50S ribosomal protein L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831)	Thermus thermophilus
25	AD, Y (AX, DX)	50S ribosomal protein L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327)	Thermus thermophilus
26	BD, Z (A4, D4)	50S ribosomal protein L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197)	Thermus thermophilus
27	AA, CD (A5, D5)	50S ribosomal protein L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783)	Thermus thermophilus
28	BA, DD (A6, D6)	50S ribosomal protein L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471)	Thermus thermophilus
29	CA, ED (A7, D7)	50S ribosomal protein L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468)	Thermus thermophilus
30	DA, FD (A8, D8)	50S ribosomal protein L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632)	Thermus thermophilus
31	DB, EA (BA, CA)	16S ribosomal RNA	polymer	1506	489002.5	2	GenBank (AP008226.1)	Thermus thermophilus
32	EB, FA (BE, CE)	30S RIBOSOMAL PROTEIN S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318)	Thermus thermophilus
33	FB, GA (BF, CF)	30S RIBOSOMAL PROTEIN S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189)	Thermus thermophilus
34	GB, HA (BG, CG)	30S RIBOSOMAL PROTEIN S4	polymer	208	24242.3	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479)	Thermus thermophilus
35	HB, IA (BH, CH)	30S RIBOSOMAL PROTEIN S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719)	Thermus thermophilus
36	IB, JA (BI, CI)	30S RIBOSOMAL PROTEIN S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250)	Thermus thermophilus
37	JB, KA (BJ, CJ)	30S RIBOSOMAL PROTEIN S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177)	Thermus thermophilus
38	KB, LA (BK, CK)	30S RIBOSOMAL PROTEIN S8	polymer	138	15868.6	2	UniProt (Q5SHQ2)	Thermus thermophilus
39	LB, MA (BL, CL)	30S RIBOSOMAL PROTEIN S9	polymer	128	14410.6	2	UniProt (P80374) Pfam (PF00380)	Thermus thermophilus
40	MB, NA (BM, CM)	30S RIBOSOMAL PROTEIN S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338)	Thermus thermophilus
41	NB, OA (BN, CN)	30S RIBOSOMAL PROTEIN S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411)	Thermus thermophilus
42	OB, PA (BO, CO)	30S RIBOSOMAL PROTEIN S12	polymer	132	14637.4	2	UniProt (Q5SHN3) Pfam (PF00164)	Thermus thermophilus
43	PB, QA (BP, CP)	30S RIBOSOMAL PROTEIN S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416)	Thermus thermophilus
44	QB, RA (BQ, CQ)	30S RIBOSOMAL PROTEIN S14	polymer	61	7158.7	2	UniProt (Q5SHQ1)	Thermus thermophilus
45	RB, SA (BR, CR)	30S RIBOSOMAL PROTEIN S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312)	Thermus thermophilus
46	SB, TA (BS, CS)	30S RIBOSOMAL PROTEIN S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886)	Thermus thermophilus
47	TB, UA (BT, CT)	30S RIBOSOMAL PROTEIN S17	polymer	105	12325.7	2	UniProt (Q5SHP7)	Thermus thermophilus
48	UB, VA (BU, CU)	30S RIBOSOMAL PROTEIN S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084)	Thermus thermophilus
49	VB, WA (BV, CV)	30S RIBOSOMAL PROTEIN S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203)	Thermus thermophilus
50	WB, XA (BW, CW)	30S RIBOSOMAL PROTEIN S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649)	Thermus thermophilus
51	XB, YA (BX, CX)	30S RIBOSOMAL PROTEIN THX	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070)	Escherichia coli
52	AC, BB, YB, ZA (BB, BD, CB, CD)	TRNA-TYR	polymer	85	27402.5	4	GenBank (AP012306.1)
53	AB, ZB (BC, CC)	TRNA-FMET	polymer	77	24801.8	2	GenBank (AP012306.1)	Escherichia coli
54	BC, CB (B1, C1)	MRNA	polymer	16	5177.2	2	GenBank (AP012306.1)
55	AAA, ABA, ABB, ACA, ADA... (AF, BA, DA, AA, CA...)	MAGNESIUM ION	non-polymer		24.3	903	Chemie (MG)
56	AAB, ACB, ADB, AGA, AHA... (DA, BA, BL, BC, DB...)	osmium (III) hexammine	non-polymer		286.4	710	Chemie (OHX)
57	BFA, XOA (BA, CA)	PAROMOMYCIN	non-polymer		615.6	2	Chemie (PAR)
58	BJA, NSA, QSA, YIA (BQ, CG, CQ, BG)	ZINC ION	non-polymer		65.4	4	Chemie (ZN)

Sequence modifications

AA, DA: 1 - 2902 (GenBank: AP008226.1)

PDB	External Database	Details
U 161	-	insertion
A 654	G 352709	conflict
C 654	G 352713	conflict
G 654	C 352724	conflict
A 654	C 352728	conflict
U 1058	G 353133	conflict
A 1080	C 353155	conflict

Contents of the asymmetric unit

Polymers	Number of chains	110
	Total formula weight	4486266.4
Non-Polymers*	Number of molecules	1619
	Total formula weight	226759.5
All*	Total formula weight	4713025.8

*Water molecules are not included.