4V8E

Crystal structure analysis of ribosomal decoding (near-cognate tRNA-tyr complex).

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)	RNA (2912-MER)	polymer	2912	947013.0	2	GenBank (AP008226.1)	Thermus thermophilus
2	B, EB (AB, CB)	5S RIBOSOMAL RNA	polymer	122	39540.6	2	GenBank (AP008226.1)	Thermus thermophilus
3	C, FB (AD, CD)	50S ribosomal protein L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947)	Thermus thermophilus
4	D, GB (AE, CE)	50S ribosomal protein L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297)	Thermus thermophilus
5	E, HB (AF, CF)	50S ribosomal protein L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573)	Thermus thermophilus
6	F, IB (AG, CG)	50S ribosomal protein L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673)	Thermus thermophilus
7	G, JB (AH, CH)	50S ribosomal protein L6	polymer	180	19568.9	2	UniProt (Q5SHQ3) Pfam (PF00347) UniProt (by SIFTS) (P0DOY8)	Thermus thermophilus
8	H, KB (AK, CK)	50S ribosomal protein L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948)	Thermus thermophilus
9	I, LB (AM, CM)	50S ribosomal protein L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572)	Thermus thermophilus
10	J, MB (AN, CN)	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238)	Thermus thermophilus
11	K, NB (AO, CO)	50S ribosomal protein L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828)	Thermus thermophilus
12	L, OB (AP, CP)	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252)	Thermus thermophilus
13	M, PB (A0, C0)	50S ribosomal protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196)	Thermus thermophilus
14	N, QB (AQ, CQ)	50S ribosomal protein L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861)	Thermus thermophilus
15	O, RB (AR, CR)	50S ribosomal protein L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245)	Thermus thermophilus
16	P, SB (A1, C1)	50S ribosomal protein L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453)	Thermus thermophilus
17	Q, TB (A2, C2)	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829)	Thermus thermophilus
18	R, UB (AS, CS)	50S ribosomal protein L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237)	Thermus thermophilus
19	S, VB (AT, CT)	50S ribosomal protein L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276)	Thermus thermophilus
20	T, WB (AU, CU)	50S ribosomal protein L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136)	Thermus thermophilus
21	U, XB (AV, CV)	50S ribosomal protein L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693)	Thermus thermophilus
22	V, YB (A3, C3)	50S ribosomal protein L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016)	Thermus thermophilus
23	W, ZB (AZ, CZ)	50S ribosomal protein L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830)	Thermus thermophilus
24	AC, X (AW, CW)	50S ribosomal protein L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831)	Thermus thermophilus
25	BC, Y (AX, CX)	50S ribosomal protein L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327)	Thermus thermophilus
26	CC, Z (A4, C4)	50S ribosomal protein L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197)	Thermus thermophilus
27	AA, DC (A5, C5)	50S ribosomal protein L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783)	Thermus thermophilus
28	BA, EC (A6, C6)	50S ribosomal protein L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471)	Thermus thermophilus
29	CA, FC (A7, C7)	50S ribosomal protein L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468)	Thermus thermophilus
30	DA, GC (A8, C8)	50S ribosomal protein L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632)	Thermus thermophilus
31	EA, HC (BA, DA)	16S ribosomal RNA	polymer	1506	489002.5	2	GenBank (AP008226.1)	Thermus thermophilus
32	FA, IC (BE, DE)	30S RIBOSOMAL PROTEIN S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318)	Thermus thermophilus
33	GA, JC (BF, DF)	30S RIBOSOMAL PROTEIN S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189)	Thermus thermophilus
34	HA, KC (BG, DG)	30S RIBOSOMAL PROTEIN S4	polymer	208	24242.3	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479)	Thermus thermophilus
35	IA, LC (BH, DH)	30S RIBOSOMAL PROTEIN S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719)	Thermus thermophilus
36	JA, MC (BI, DI)	30S RIBOSOMAL PROTEIN S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250)	Thermus thermophilus
37	KA, NC (BJ, DJ)	30S RIBOSOMAL PROTEIN S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177)	Thermus thermophilus
38	LA, OC (BK, DK)	30S RIBOSOMAL PROTEIN S8	polymer	138	15868.6	2	UniProt (Q5SHQ2) Pfam (PF00410) UniProt (by SIFTS) (P0DOY9)	Thermus thermophilus
39	MA, PC (BL, DL)	30S RIBOSOMAL PROTEIN S9	polymer	128	14410.6	2	UniProt (P80374) Pfam (PF00380)	Thermus thermophilus
40	NA, QC (BM, DM)	30S RIBOSOMAL PROTEIN S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338)	Thermus thermophilus
41	OA, RC (BN, DN)	30S RIBOSOMAL PROTEIN S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411)	Thermus thermophilus
42	PA, SC (BO, DO)	30S RIBOSOMAL PROTEIN S12	polymer	132	14637.4	2	UniProt (Q5SHN3) Pfam (PF00164)	Thermus thermophilus
43	QA, TC (BP, DP)	30S RIBOSOMAL PROTEIN S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416)	Thermus thermophilus
44	RA, UC (BQ, DQ)	30S RIBOSOMAL PROTEIN S14	polymer	61	7158.7	2	UniProt (Q5SHQ1) Pfam (PF00253) UniProt (by SIFTS) (P0DOY6)	Thermus thermophilus
45	SA, VC (BR, DR)	30S RIBOSOMAL PROTEIN S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312)	Thermus thermophilus
46	TA, WC (BS, DS)	30S RIBOSOMAL PROTEIN S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886)	Thermus thermophilus
47	UA, XC (BT, DT)	30S RIBOSOMAL PROTEIN S17	polymer	105	12325.7	2	UniProt (Q5SHP7) Pfam (PF00366) UniProt (by SIFTS) (P0DOY7)	Thermus thermophilus
48	VA, YC (BU, DU)	30S RIBOSOMAL PROTEIN S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084)	Thermus thermophilus
49	WA, ZC (BV, DV)	30S RIBOSOMAL PROTEIN S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203)	Thermus thermophilus
50	AD, XA (BW, DW)	30S RIBOSOMAL PROTEIN S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649)	Thermus thermophilus
51	BD, YA (BX, DX)	30S RIBOSOMAL PROTEIN THX	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070)	Escherichia coli
52	BB, CD, ED, ZA (BB, BD, DB, DD)	TRNA-TYR	polymer	85	27402.5	4	GenBank (AP012306.1)
53	AB, DD (BC, DC)	TRNA-FMET	polymer	77	24801.8	2	GenBank (AP012306.1)	Escherichia coli
54	CB, FD (B1, D1)	MRNA	polymer	16	5177.2	2
55	AAA, ABA, ABB, ACA, ADB... (AF, BA, CA, CB, AA...)	MAGNESIUM ION	non-polymer		24.3	894	Chemie (MG)
56	AAB, ACB, ADA, AEA, AHA... (CA, BA, BG, DA, DC...)	osmium (III) hexammine	non-polymer		286.4	712	Chemie (OHX)
57	DJA, FMB, KMB, ZIA (BQ, DG, DQ, BG)	ZINC ION	non-polymer		65.4	4	Chemie (ZN)

Sequence modifications

AA, CA: 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

BC, DC: 1 - 77 (GenBank: AP012306.1)

PDB	External Database	Details
C 18	U 2457939	conflict

Contents of the asymmetric unit

Polymers	Number of chains	110
	Total formula weight	4486266.4
Non-Polymers*	Number of molecules	1610
	Total formula weight	225882.2
All*	Total formula weight	4712148.5

*Water molecules are not included.