4U25

Crystal structure of the E. coli ribosome bound to virginiamycin M1.

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, BB (AA, CA)	16S rRNA	polymer	1539	498725.4	2	GenBank (359330873)	Escherichia coli str. K-12 substr. MDS42
2	B, CB (AB, CB)	30S ribosomal protein S2	polymer	218	24253.9	2	UniProt (P0A7V0) Pfam (PF00318)	Escherichia coli
3	C, DB (AC, CC)	30S ribosomal protein S3	polymer	206	23078.8	2	UniProt (P0A7V3) Pfam (PF07650) Pfam (PF00189)	Escherichia coli
4	D, EB (AD, CD)	30S ribosomal protein S4	polymer	205	23383.0	2	UniProt (P0A7V8) Pfam (PF00163) Pfam (PF01479)	Escherichia coli
5	E, FB (AE, CE)	30S ribosomal protein S5	polymer	150	15804.3	2	UniProt (P0A7W1) Pfam (PF00333) Pfam (PF03719)	Escherichia coli
6	F, GB (AF, CF)	30S ribosomal protein S6	polymer	100	11669.4	2	UniProt (P02358) Pfam (PF01250)	Escherichia coli
7	G, HB (AG, CG)	30S ribosomal protein S7	polymer	151	16861.5	2	UniProt (P02359) Pfam (PF00177)	Escherichia coli
8	H, IB (AH, CH)	30S ribosomal protein S8	polymer	129	14015.4	2	UniProt (P0A7W7) Pfam (PF00410)	Escherichia coli
9	I, JB (AI, CI)	30S ribosomal protein S9	polymer	127	14554.9	2	UniProt (P0A7X3) Pfam (PF00380)	Escherichia coli
10	J, KB (AJ, CJ)	30S ribosomal protein S10	polymer	98	11197.0	2	UniProt (P0A7R5) Pfam (PF00338)	Escherichia coli
11	K, LB (AK, CK)	30S ribosomal protein S11	polymer	117	12487.2	2	UniProt (P0A7R9) Pfam (PF00411)	Escherichia coli
12	L, MB (AL, CL)	30S ribosomal protein S12	polymer	123	13637.0	2	UniProt (P0A7S3) Pfam (PF00164)	Escherichia coli
13	M, NB (AM, CM)	30S ribosomal protein S13	polymer	114	12625.8	2	UniProt (P0A7S9) Pfam (PF00416)	Escherichia coli
14	N, OB (AN, CN)	30S ribosomal protein S14	polymer	100	11475.4	2	UniProt (P0AG59) Pfam (PF00253)	Escherichia coli
15	O, PB (AO, CO)	30S ribosomal protein S15	polymer	88	10159.6	2	UniProt (P0ADZ4) Pfam (PF00312)	Escherichia coli
16	P, QB (AP, CP)	30S ribosomal protein S16	polymer	82	9207.6	2	UniProt (P0A7T3) Pfam (PF00886)	Escherichia coli
17	Q, RB (AQ, CQ)	30S ribosomal protein S17	polymer	80	9263.9	2	UniProt (P0AG63) Pfam (PF00366)	Escherichia coli
18	R, SB (AR, CR)	30S ribosomal protein S18	polymer	55	6466.5	2	UniProt (P0A7T7) Pfam (PF01084)	Escherichia coli
19	S, TB (AS, CS)	30S ribosomal protein S19	polymer	79	9057.6	2	UniProt (P0A7U3) Pfam (PF00203)	Escherichia coli
20	T, UB (AT, CT)	30S ribosomal protein S20	polymer	85	9506.2	2	UniProt (P0A7U7) Pfam (PF01649)	Escherichia coli
21	U, VB (AU, CU)	30S ribosomal protein S21	polymer	51	6067.1	2	UniProt (P68679) Pfam (PF01165)	Escherichia coli
22	V, WB (BA, DA)	23S rRNA	polymer	2903	941306.2	2	GenBank (359330873)	Escherichia coli str. K-12 substr. MDS42
23	W, XB (BB, DB)	5S rRNA	polymer	119	38483.9	2	GenBank (359330873)	Escherichia coli str. K-12 substr. MDS42
24	X, YB (BC, DC)	50S ribosomal protein L2	polymer	271	29663.2	2	UniProt (P60422) Pfam (PF00181) Pfam (PF03947)	Escherichia coli
25	Y, ZB (BD, DD)	50S ribosomal protein L3	polymer	209	22277.5	2	UniProt (P60438) Pfam (PF00297)	Escherichia coli
26	AC, Z (BE, DE)	50S ribosomal protein L4	polymer	201	22121.6	2	UniProt (P60723) Pfam (PF00573)	Escherichia coli
27	AA, BC (BF, DF)	50S ribosomal protein L5	polymer	177	20073.2	2	UniProt (P62399) Pfam (PF00281) Pfam (PF00673)	Escherichia coli
28	BA, CC (BG, DG)	50S ribosomal protein L6	polymer	176	18801.6	2	UniProt (P0AG55) Pfam (PF00347)	Escherichia coli
29	CA, DC (BH, DH)	50S ribosomal protein L9	polymer	149	15789.0	2	UniProt (P0A7R1) Pfam (PF01281) Pfam (PF03948)	Escherichia coli
30	DA, EC (BI, DI)	50S ribosomal protein L11	polymer	141	14763.2	2	UniProt (P0A7J7) Pfam (PF03946) Pfam (PF00298)	Escherichia coli
31	EA, FC (BJ, DJ)	50S ribosomal protein L13	polymer	142	16050.6	2	UniProt (P0AA10) Pfam (PF00572)	Escherichia coli
32	FA, GC (BK, DK)	50S ribosomal protein L14	polymer	122	13451.9	2	UniProt (P0ADY3) Pfam (PF00238)	Escherichia coli
33	GA, HC (BL, DL)	50S ribosomal protein L15	polymer	143	14877.3	2	UniProt (P02413) Pfam (PF00828)	Escherichia coli
34	HA, IC (BM, DM)	50S ribosomal protein L16	polymer	136	15312.3	2	UniProt (P0ADY7) Pfam (PF00252)	Escherichia coli
35	IA, JC (BN, DN)	50S ribosomal protein L17	polymer	120	13721.9	2	UniProt (P0AG44) Pfam (PF01196)	Escherichia coli
36	JA, KC (BO, DO)	50S ribosomal protein L18	polymer	116	12663.5	2	UniProt (P0C018) Pfam (PF00861)	Escherichia coli
37	KA, LC (BP, DP)	50S ribosomal protein L19	polymer	114	13028.1	2	UniProt (P0A7K6) Pfam (PF01245)	Escherichia coli
38	LA, MC (BQ, DQ)	50S ribosomal protein L20	polymer	117	13396.8	2	UniProt (P0A7L3) Pfam (PF00453)	Escherichia coli
39	MA, NC (BR, DR)	50S ribosomal protein L21	polymer	103	11586.4	2	UniProt (P0AG48) Pfam (PF00829)	Escherichia coli
40	NA, OC (BS, DS)	50S ribosomal protein L22	polymer	110	12253.4	2	UniProt (P61175) Pfam (PF00237)	Escherichia coli
41	OA, PC (BT, DT)	50S ribosomal protein L23	polymer	93	10546.5	2	UniProt (P0ADZ0) Pfam (PF00276)	Escherichia coli
42	PA, QC (BU, DU)	50S ribosomal protein L24	polymer	102	11078.9	2	UniProt (P60624) Pfam (PF00467) Pfam (PF17136)	Escherichia coli
43	QA, RC (BV, DV)	50S ribosomal protein L25	polymer	94	10713.5	2	UniProt (P68919) Pfam (PF01386)	Escherichia coli
44	RA, SC (BW, DW)	50S ribosomal protein L27	polymer	76	8275.5	2	UniProt (P0A7L8) Pfam (PF01016)	Escherichia coli
45	SA, TC (BX, DX)	50S ribosomal protein L28	polymer	77	8896.4	2	UniProt (P0A7M2) Pfam (PF00830)	Escherichia coli
46	TA, UC (BY, DY)	50S ribosomal protein L29	polymer	63	7286.5	2	UniProt (P0A7M6) Pfam (PF00831)	Escherichia coli
47	UA, VC (BZ, DZ)	50S ribosomal protein L30	polymer	58	6423.6	2	UniProt (P0AG51) Pfam (PF00327)	Escherichia coli
48	VA, WC (B0, D0)	50S ribosomal protein L32	polymer	56	6332.2	2	UniProt (P0A7N4) Pfam (PF01783)	Escherichia coli
49	WA, XC (B1, D1)	50S ribosomal protein L33	polymer	50	5814.8	2	UniProt (P0A7N9) Pfam (PF00471)	Escherichia coli
50	XA, YC (B2, D2)	50S ribosomal protein L34	polymer	46	5397.5	2	UniProt (P0A7P5) Pfam (PF00468)	Escherichia coli
51	YA, ZC (B3, D3)	50S ribosomal protein L35	polymer	64	7181.8	2	UniProt (P0A7Q1) Pfam (PF01632)	Escherichia coli	Ribosomal protein A
52	AD, ZA (B4, D4)	50S ribosomal protein L36	polymer	38	4377.4	2	UniProt (P0A7Q6) Pfam (PF00444)	Escherichia coli	Ribosomal protein B
53	AB (B5)	50S ribosomal protein L1	polymer	228	24741.5	1	UniProt (Q5SLP7) Pfam (PF00687)	Thermus thermophilus
54	AE, AF, AG, AH, AI... (AA, BA, CA, DA, DB...)	MAGNESIUM ION	non-polymer		24.3	498	Chemie (MG)
55	SP, VF (DA, BA)	VIRGINIAMYCIN M1	non-polymer		525.6	2	Chemie (VIR)
56	IW, NN (D4, B4)	ZINC ION	non-polymer		65.4	2	Chemie (ZN)
57	AX, BX, CX, DX, EX... (BV, B2, B3, B4, CA...)	water	water		18.0	1723	Chemie (HOH)

Contents of the asymmetric unit

Polymers	Number of chains	105
	Total formula weight	4255628.4
Non-Polymers*	Number of molecules	502
	Total formula weight	13285.9
All*	Total formula weight	4268914.3

*Water molecules are not included.