5J8A

Structure of the E coli 70S ribosome with the U1052G mutation in 16S rRNA bound to tigecycline

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, BA (AA, BA)	16S rRNA	polymer	1534	497445.0	2	GenBank (675819282)	Escherichia coli
2	B, CA (AB, BB)	30S ribosomal protein S2	polymer	224	24971.8	2	UniProt (P0A7V0) Pfam (PF00318)	Escherichia coli (strain K12)
3	C, DA (AC, BC)	30S ribosomal protein S3	polymer	206	23078.8	2	UniProt (P0A7V3) Pfam (PF07650) Pfam (PF00189)	Escherichia coli (strain K12)
4	D, EA (AD, BD)	30S ribosomal protein S4	polymer	205	23383.0	2	UniProt (P0A7V8) Pfam (PF00163) Pfam (PF01479)	Escherichia coli (strain K12)
5	E, FA (AE, BE)	30S ribosomal protein S5	polymer	155	16361.9	2	UniProt (P0A7W1) Pfam (PF00333) Pfam (PF03719)	Escherichia coli (strain K12)
6	F, GA (AF, BF)	30S ribosomal protein S6	polymer	106	12326.3	2	UniProt (P02358) Pfam (PF01250)	Escherichia coli (strain K12)
7	G, HA (AG, BG)	30S ribosomal protein S7	polymer	151	16861.5	2	UniProt (P02359) Pfam (PF00177)	Escherichia coli (strain K12)
8	H, IA (AH, BH)	30S ribosomal protein S8	polymer	129	14015.4	2	UniProt (P0A7W7) Pfam (PF00410)	Escherichia coli (strain K12)
9	I, JA (AI, BI)	30S ribosomal protein S9	polymer	127	14554.9	2	UniProt (P0A7X3) Pfam (PF00380)	Escherichia coli (strain K12)
10	J, KA (AJ, BJ)	30S ribosomal protein S10	polymer	99	11325.1	2	UniProt (P0A7R5) Pfam (PF00338)	Escherichia coli (strain K12)
11	K, LA (AK, BK)	30S ribosomal protein S11	polymer	117	12487.2	2	UniProt (P0A7R9) Pfam (PF00411)	Escherichia coli (strain K12)
12	L, MA (AL, BL)	30S ribosomal protein S12	polymer	123	13683.1	2	UniProt (P0A7S3) Pfam (PF00164)	Escherichia coli (strain K12)
13	M, NA (AM, BM)	30S ribosomal protein S13	polymer	114	12625.8	2	UniProt (P0A7S9) Pfam (PF00416)	Escherichia coli (strain K12)
14	N, OA (AN, BN)	30S ribosomal protein S14	polymer	100	11475.4	2	UniProt (P0AG59) Pfam (PF00253)	Escherichia coli (strain K12)
15	O, PA (AO, BO)	30S ribosomal protein S15	polymer	88	10159.6	2	UniProt (P0ADZ4) Pfam (PF00312)	Escherichia coli (strain K12)
16	P, QA (AP, BP)	30S ribosomal protein S16	polymer	82	9207.6	2	UniProt (P0A7T3) Pfam (PF00886)	Escherichia coli (strain K12)
17	Q, RA (AQ, BQ)	30S ribosomal protein S17	polymer	80	9263.9	2	UniProt (P0AG63) Pfam (PF00366)	Escherichia coli (strain K12)
18	R, SA (AR, BR)	30S ribosomal protein S18	polymer	55	6466.5	2	UniProt (P0A7T7) Pfam (PF01084)	Escherichia coli (strain K12)
19	S, TA (AS, BS)	30S ribosomal protein S19	polymer	79	9057.6	2	UniProt (P0A7U3) Pfam (PF00203)	Escherichia coli (strain K12)
20	T, UA (AT, BT)	30S ribosomal protein S20	polymer	86	9577.3	2	UniProt (P0A7U7) Pfam (PF01649)	Escherichia coli (strain K12)
21	U, VA (AU, BU)	30S ribosomal protein S21	polymer	56	6629.7	2	UniProt (P68679) Pfam (PF01165)	Escherichia coli (strain K12)
22	V, WA (C1, D1)	50S ribosomal protein L32	polymer	56	6332.2	2	UniProt (P0A7N4) Pfam (PF01783)	Escherichia coli (strain K12)
23	W, XA (C2, D2)	50S ribosomal protein L33	polymer	51	5928.0	2	UniProt (P0A7N9) Pfam (PF00471)	Escherichia coli (strain K12)
24	X, YA (C3, D3)	50S ribosomal protein L34	polymer	46	5397.5	2	UniProt (P0A7P5) Pfam (PF00468)	Escherichia coli (strain K12)
25	Y, ZA (C4, D4)	50S ribosomal protein L35	polymer	64	7181.8	2	UniProt (P0A7Q1) Pfam (PF01632)	Escherichia coli (strain K12)	Ribosomal protein A
26	AB, Z (C5, D5)	50S ribosomal protein L36	polymer	38	4377.4	2	UniProt (P0A7Q6) Pfam (PF00444)	Escherichia coli (strain K12)	Ribosomal protein B
27	AA, BB (C0, D0)	50S ribosomal protein L30	polymer	58	6423.6	2	UniProt (P0AG51) Pfam (PF00327)	Escherichia coli (strain K12)
28	CB, ZC (CB, DB)	5S rRNA	polymer	120	38790.1	2	GenBank (937521852)	Escherichia coli
29	DB, GB (CC, DC)	50S ribosomal protein L2	polymer	272	29792.4	2	UniProt (P60422) Pfam (PF00181) Pfam (PF03947)	Escherichia coli (strain K12)
30	EB (CD)	50S ribosomal protein L3	polymer	209	22277.5	1	UniProt (P60438) Pfam (PF00297)	Escherichia coli (strain K12)
31	FB (CA)	23S rRNA	polymer	2904	941810.6	1	GenBank (42756)	Escherichia coli
32	HB (DD)	50S ribosomal protein L3	polymer	209	22291.6	1	UniProt (P60438) Pfam (PF00297)	Escherichia coli (strain K12)
33	DC, IB (CE, DE)	50S ribosomal protein L4	polymer	201	22121.6	2	UniProt (P60723) Pfam (PF00573)	Escherichia coli (strain K12)
34	EC, JB (CF, DF)	50S ribosomal protein L5	polymer	178	20202.4	2	UniProt (P62399) Pfam (PF00281) Pfam (PF00673)	Escherichia coli (strain K12)
35	FC, KB (CG, DG)	50S ribosomal protein L6	polymer	176	18801.6	2	UniProt (P0AG55) Pfam (PF00347)	Escherichia coli (strain K12)
36	GC, LB (CH, DH)	50S ribosomal protein L9	polymer	149	15789.0	2	UniProt (P0A7R1) Pfam (PF01281) Pfam (PF03948)	Escherichia coli (strain K12)
37	HC, MB (CJ, DJ)	50S ribosomal protein L11	polymer	135	14135.4	2	UniProt (P0A7J7) Pfam (PF03946) Pfam (PF00298)	Escherichia coli (strain K12)
38	IC, NB (CK, DK)	50S ribosomal protein L13	polymer	142	16050.6	2	UniProt (P0AA10) Pfam (PF00572)	Escherichia coli (strain K12)
39	JC, OB (CL, DL)	50S ribosomal protein L14	polymer	123	13565.1	2	UniProt (P0ADY3) Pfam (PF00238)	Escherichia coli (strain K12)
40	KC, PB (CM, DM)	50S ribosomal protein L15	polymer	144	15008.5	2	UniProt (P02413) Pfam (PF00828)	Escherichia coli (strain K12)
41	LC, QB (CN, DN)	50S ribosomal protein L16	polymer	136	15327.3	2	UniProt (P0ADY7) Pfam (PF00252)	Escherichia coli (strain K12)
42	MC, RB (CO, DO)	50S ribosomal protein L17	polymer	125	14193.5	2	UniProt (P0AG44) Pfam (PF01196)	Escherichia coli (strain K12)
43	NC, SB (CP, DP)	50S ribosomal protein L18	polymer	117	12794.7	2	UniProt (P0C018) Pfam (PF00861)	Escherichia coli (strain K12)
44	OC, TB (CQ, DQ)	50S ribosomal protein L19	polymer	114	13028.1	2	UniProt (P0A7K6) Pfam (PF01245)	Escherichia coli (strain K12)
45	PC, UB (CR, DR)	50S ribosomal protein L20	polymer	117	13396.8	2	UniProt (P0A7L3) Pfam (PF00453)	Escherichia coli (strain K12)
46	QC, VB (CS, DS)	50S ribosomal protein L21	polymer	103	11586.4	2	UniProt (P0AG48) Pfam (PF00829)	Escherichia coli (strain K12)
47	RC, WB (CT, DT)	50S ribosomal protein L22	polymer	110	12253.4	2	UniProt (P61175) Pfam (PF00237)	Escherichia coli (strain K12)
48	SC, XB (CU, DU)	50S ribosomal protein L23	polymer	93	10546.5	2	UniProt (P0ADZ0) Pfam (PF00276)	Escherichia coli (strain K12)
49	TC, YB (CV, DV)	50S ribosomal protein L24	polymer	103	11208.1	2	UniProt (P60624) Pfam (PF00467) Pfam (PF17136)	Escherichia coli (strain K12)
50	UC, ZB (CW, DW)	50S ribosomal protein L25	polymer	94	10713.5	2	UniProt (A7ZP09) Pfam (PF01386) UniProt (by SIFTS) (P68919)	Escherichia coli O139:H28 (strain E24377A / ETEC)
51	AC, VC (CX, DX)	50S ribosomal protein L27	polymer	83	8944.3	2	UniProt (P0A7L8) Pfam (PF01016)	Escherichia coli (strain K12)
52	BC, WC (CY, DY)	50S ribosomal protein L28	polymer	77	8896.4	2	UniProt (P0A7M2) Pfam (PF00830)	Escherichia coli (strain K12)
53	CC, XC (CZ, DZ)	50S ribosomal protein L29	polymer	62	7155.3	2	UniProt (P0A7M6) Pfam (PF00831)	Escherichia coli (strain K12)
54	YC (DI)	50S ribosomal protein L10	polymer	135	14568.7	1	UniProt (P0A7J3) Pfam (PF00466)	Escherichia coli (strain K12)	50S ribosomal protein L8
55	AD (DA)	23S rRNA	polymer	2904	941812.6	1	GenBank (42756)	Escherichia coli
56	AE, AF, AG, AH, AI... (AA, BA, CA, DA, DB...)	MAGNESIUM ION	non-polymer		24.3	472	Chemie (MG)
57	SF, TO, VH, VO, WX... (AA, DQ, BA, DR, DA...)	TETRAETHYLENE GLYCOL	non-polymer		194.2	7	Chemie (PG4)
58	AP, KX, LO, MO, NO... (DT, DA, DE, DK, DN...)	(4S)-2-METHYL-2,4-PENTANEDIOL	non-polymer		118.2	14	Chemie (MPD)
59	BX, BY, CY, DY, LX... (DA, AA)	1,4-DIAMINOBUTANE	non-polymer		88.2	16	Chemie (PUT)
60	CG, WH (AA, BA)	TIGECYCLINE	non-polymer		587.7	2	Chemie (T1C)
61	DG, FG, GI (AB, C5, D5)	ZINC ION	non-polymer		65.4	3	Chemie (ZN)
62	DI, EG, FI, FX, GX... (D1, AL, D3, DA, DL...)	DI(HYDROXYETHYL)ETHER	non-polymer		106.1	11	Chemie (PEG)
63	AX, BI, CP, DX, EX... (DA, D1, DB)	1,2-ETHANEDIOL	non-polymer		62.1	12	Chemie (EDO)
64	BP, CI, EI, FY, JX... (DU, D1, D3, DA, DS)	TRIETHYLENE GLYCOL	non-polymer		150.2	9	Chemie (PGE)
65	EY, MX, PW, TW (DA)	SPERMIDINE	non-polymer		145.2	4	Chemie (SPD)
66	IX, RW (DA)	PENTAETHYLENE GLYCOL	non-polymer		238.3	2	Chemie (1PE)
67	CX, HX, XW (DA)	ACETIC ACID	non-polymer		60.1	3	Chemie (ACY)
68	RX (DA)	GUANINE	non-polymer		151.1	1	Chemie (GUN)
69	AY (DA)	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL	non-polymer		122.1	1	Chemie (TRS)
70	AAA, ABA, AZ, BAA, BBA... (DC, DW, AR, DD, DX...)	water	water		18.0	7744	Chemie (HOH)

Sequence modifications

AA, BA: 1 - 1534 (GenBank: 675819282)

PDB	External Database	Details
G 1052	U 37364	engineered mutation

CN, DN: 1 - 136 (UniProt: P0ADY7)

PDB	External Database	Details
4d4 81	Arg 81	conflict

DI: 2 - 136 (UniProt: P0A7J3)

PDB	External Database	Details
Val 85	Ser 85	conflict
Thr 86	Met 86	conflict

Contents of the asymmetric unit

Polymers	Number of chains	105
	Total formula weight	4252557.5
Non-Polymers*	Number of molecules	557
	Total formula weight	22042.6
All*	Total formula weight	4274600.1

*Water molecules are not included.