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	AA, CA	RNA (2912-MER)	polymer	2912	947013.0	2	GenBank (AP008226.1)	Thermus thermophilus
2	AB, CB	5S RIBOSOMAL RNA	polymer	122	39540.6	2	GenBank (AP008226.1)	Thermus thermophilus
3	AD, CD	50S ribosomal protein L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947) In PDB	Thermus thermophilus
4	AE, CE	50S ribosomal protein L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297) In PDB	Thermus thermophilus
5	AF, CF	50S ribosomal protein L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573) In PDB	Thermus thermophilus
6	AG, CG	50S ribosomal protein L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673) In PDB	Thermus thermophilus
7	AH, CH	50S ribosomal protein L6	polymer	180	19568.9	2	UniProt (Q5SHQ3) In PDB	Thermus thermophilus
8	AK, CK	50S ribosomal protein L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948) In PDB	Thermus thermophilus
9	AM, CM	50S ribosomal protein L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572) In PDB	Thermus thermophilus
10	AN, CN	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238) In PDB	Thermus thermophilus
11	AO, CO	50S ribosomal protein L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828) In PDB	Thermus thermophilus
12	AP, CP	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252) In PDB	Thermus thermophilus
13	A0, C0	50S ribosomal protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196) In PDB	Thermus thermophilus
14	AQ, CQ	50S ribosomal protein L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861) In PDB	Thermus thermophilus
15	AR, CR	50S ribosomal protein L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245) In PDB	Thermus thermophilus
16	A1, C1	50S ribosomal protein L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453) In PDB	Thermus thermophilus
17	A2, C2	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829) In PDB	Thermus thermophilus
18	AS, CS	50S ribosomal protein L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237) In PDB	Thermus thermophilus
19	AT, CT	50S ribosomal protein L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276) In PDB	Thermus thermophilus
20	AU, CU	50S ribosomal protein L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136) In PDB	Thermus thermophilus
21	AV, CV	50S ribosomal protein L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693) In PDB	Thermus thermophilus
22	A3, C3	50S ribosomal protein L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016) In PDB	Thermus thermophilus
23	AZ, CZ	50S ribosomal protein L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830) In PDB	Thermus thermophilus
24	AW, CW	50S ribosomal protein L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831) In PDB	Thermus thermophilus
25	AX, CX	50S ribosomal protein L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327) In PDB	Thermus thermophilus
26	A4, C4	50S ribosomal protein L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197) In PDB	Thermus thermophilus
27	A5, C5	50S ribosomal protein L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783) In PDB	Thermus thermophilus
28	A6, C6	50S ribosomal protein L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471) In PDB	Thermus thermophilus
29	A7, C7	50S ribosomal protein L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468) In PDB	Thermus thermophilus
30	A8, C8	50S ribosomal protein L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632) In PDB	Thermus thermophilus
31	BA, DA	16S ribosomal RNA	polymer	1506	489002.5	2	GenBank (AP008226.1)	Thermus thermophilus
32	BE, DE	30S RIBOSOMAL PROTEIN S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318) In PDB	Thermus thermophilus
33	BF, DF	30S RIBOSOMAL PROTEIN S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189) In PDB	Thermus thermophilus
34	BG, DG	30S RIBOSOMAL PROTEIN S4	polymer	208	24242.3	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479) In PDB	Thermus thermophilus
35	BH, DH	30S RIBOSOMAL PROTEIN S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719) In PDB	Thermus thermophilus
36	BI, DI	30S RIBOSOMAL PROTEIN S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250) In PDB	Thermus thermophilus
37	BJ, DJ	30S RIBOSOMAL PROTEIN S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177) In PDB	Thermus thermophilus
38	BK, DK	30S RIBOSOMAL PROTEIN S8	polymer	138	15868.6	2	UniProt (Q5SHQ2) In PDB	Thermus thermophilus
39	BL, DL	30S RIBOSOMAL PROTEIN S9	polymer	128	14410.6	2	UniProt (P80374) Pfam (PF00380) In PDB	Thermus thermophilus
40	BM, DM	30S RIBOSOMAL PROTEIN S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338) In PDB	Thermus thermophilus
41	BN, DN	30S RIBOSOMAL PROTEIN S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411) In PDB	Thermus thermophilus
42	BO, DO	30S RIBOSOMAL PROTEIN S12	polymer	132	14637.4	2	UniProt (Q5SHN3) Pfam (PF00164) In PDB	Thermus thermophilus
43	BP, DP	30S RIBOSOMAL PROTEIN S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416) In PDB	Thermus thermophilus
44	BQ, DQ	30S RIBOSOMAL PROTEIN S14	polymer	61	7158.7	2	UniProt (Q5SHQ1) In PDB	Thermus thermophilus
45	BR, DR	30S RIBOSOMAL PROTEIN S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312) In PDB	Thermus thermophilus
46	BS, DS	30S RIBOSOMAL PROTEIN S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886) In PDB	Thermus thermophilus
47	BT, DT	30S RIBOSOMAL PROTEIN S17	polymer	105	12325.7	2	UniProt (Q5SHP7) In PDB	Thermus thermophilus
48	BU, DU	30S RIBOSOMAL PROTEIN S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084) In PDB	Thermus thermophilus
49	BV, DV	30S RIBOSOMAL PROTEIN S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203) In PDB	Thermus thermophilus
50	BW, DW	30S RIBOSOMAL PROTEIN S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649) In PDB	Thermus thermophilus
51	BX, DX	30S RIBOSOMAL PROTEIN THX	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070) In PDB	Escherichia coli
52	BB, BD, DB, DD	TRNA-TYR	polymer	85	27402.5	4	GenBank (AP012306.1)
53	BC, DC	TRNA-FMET	polymer	77	24801.8	2	GenBank (AP012306.1)	Escherichia coli
54	B1, D1	MRNA	polymer	16	5177.2	2
55	AF, BA, CA, CB, AA...	MAGNESIUM ION	non-polymer		24.3	894	Chemie (MG)
56	CA, BA, BG, DA, DC...	osmium (III) hexammine	non-polymer		286.4	712	Chemie (OHX)
57	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.