4WT8

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA 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 (A2)	mRNA	polymer	9	2840.8	1		Thermus thermophilus
2	B, Y (AA, BA)	30S ribosomal protein S2	polymer	234	26987.3	2	UniProt (P80371) Pfam (PF00318)	Thermus thermophilus
3	C (AC)	30S ribosomal protein S3	polymer	238	26622.0	1	UniProt (P80372) Pfam (PF07650) Pfam (PF00189)	Thermus thermophilus
4	AA, D (AD, BD)	30S ribosomal protein S4	polymer	208	24242.3	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479)	Thermus thermophilus
5	BA, E (AE, BE)	30S ribosomal protein S5	polymer	150	16331.1	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719)	Thermus thermophilus
6	CA, F (AF, BF)	30S ribosomal protein S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250)	Thermus thermophilus	TS9
7	DA, G (AG, BG)	30S ribosomal protein S7	polymer	155	17919.8	2	UniProt (P17291) Pfam (PF00177)	Thermus thermophilus
8	EA, H (AH, BH)	30S ribosomal protein S8	polymer	138	15868.6	2	UniProt (Q5SHQ2) Pfam (PF00410) UniProt (by SIFTS) (P0DOY9)	Thermus thermophilus
9	FA, I (AI, BI)	30S ribosomal protein S9	polymer	127	14298.5	2	UniProt (P62669) UniProt (P80374) Pfam (PF00380)	Thermus thermophilus
10	GA, J (AJ, BJ)	30S ribosomal protein S10	polymer	98	11299.2	2	UniProt (Q5SHN7) Pfam (PF00338)	Thermus thermophilus
11	HA, K (AK, BK)	30S ribosomal protein S11	polymer	119	12606.4	2	UniProt (P80376) Pfam (PF00411)	Thermus thermophilus
12	IA, L (AL, BL)	30S ribosomal protein S12	polymer	124	13804.3	2	UniProt (Q5SHN3) Pfam (PF00164)	Thermus thermophilus
13	JA, M (AM, BM)	30S ribosomal protein S13	polymer	124	14078.5	2	UniProt (P80377) Pfam (PF00416)	Thermus thermophilus
14	KA, N (AN, BN)	30S ribosomal protein S14 type Z	polymer	60	7027.5	2	UniProt (Q5SHQ1) Pfam (PF00253) UniProt (by SIFTS) (P0DOY6)	Thermus thermophilus
15	LA, O (AO, BO)	30S ribosomal protein S15	polymer	88	10447.2	2	UniProt (Q5SJ76) Pfam (PF00312)	Thermus thermophilus
16	MA, P (AP, BP)	30S ribosomal protein S16	polymer	83	9924.5	2	UniProt (Q5SJH3) Pfam (PF00886)	Thermus thermophilus
17	NA, Q (AR, BR)	30S ribosomal protein S17	polymer	99	11722.9	2	UniProt (Q5SHP7) Pfam (PF00366) UniProt (by SIFTS) (P0DOY7)	Thermus thermophilus
18	OA, R (AS, BS)	30S ribosomal protein S18	polymer	70	8155.8	2	UniProt (Q5SLQ0) Pfam (PF01084)	Thermus thermophilus
19	PA, S (AT, BT)	30S ribosomal protein S19	polymer	78	8949.4	2	UniProt (Q5SHP2) Pfam (PF00203)	Thermus thermophilus
20	QA, T (AU, BU)	30S ribosomal protein S20	polymer	99	10921.1	2	UniProt (P80380) Pfam (PF01649)	Thermus thermophilus
21	RA, U (AW, BW)	30S ribosomal protein Thx	polymer	24	2960.5	2	UniProt (Q5SIH3) Pfam (PF17070)	Thermus thermophilus	S31
22	V, X (Ab, Bb)	RNA (1504-MER)	polymer	1504	488391.2	2	GenBank (55771382) GenBank (155076)	Thermus thermophilus
23	W (B2)	mRNA	polymer	10	3170.0	1		Thermus thermophilus
24	Z (BC)	30S ribosomal protein S3	polymer	206	22862.4	1	UniProt (P80372) Pfam (PF07650) Pfam (PF00189)	Thermus thermophilus
25	DC, SA, TA (C2, C3, D3)	A site tNA, E site tNA	polymer	76	24485.5	3		Thermus thermophilus
26	UA (C4)	P site trNA	polymer	77	24802.8	1		Thermus thermophilus
27	VA (CA)	50S ribosomal protein L1	polymer	206	19880.5	1	UniProt (Q5SLP7) Pfam (PF00687)	Thermus thermophilus
28	GC, WA (CB, DB)	50S ribosomal protein L2	polymer	271	29828.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947)	Thermus thermophilus
29	HC, XA (CC, DC)	50S ribosomal protein L3	polymer	204	22250.0	2	UniProt (Q5SHN8) Pfam (PF00297)	Thermus thermophilus
30	IC, YA (CD, DD)	50S ribosomal protein L4	polymer	207	23014.7	2	UniProt (Q5SHN9) Pfam (PF00573)	Thermus thermophilus	L1e
31	JC, ZA (CE, DE)	50S ribosomal protein L5	polymer	181	20930.4	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673)	Thermus thermophilus
32	AB, KC (CF, DF)	50S ribosomal protein L6	polymer	159	17363.1	2	UniProt (Q5SHQ3) Pfam (PF00347) UniProt (by SIFTS) (P0DOY8)	Thermus thermophilus
33	BB, LC (CI, DI)	50S ribosomal protein L9	polymer	145	16093.9	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948)	Thermus thermophilus
34	CB, MC (CJ, DJ)	ribosomal L10 protein	polymer	130	11081.7	2		Thermus thermophilus
35	DB, NC (CM, DM)	50S ribosomal protein L13	polymer	138	15699.7	2	UniProt (P60488) Pfam (PF00572)	Thermus thermophilus
36	EB, OC (CN, DN)	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238)	Thermus thermophilus
37	FB, PC (CO, DO)	50S ribosomal protein L15	polymer	146	15858.5	2	UniProt (Q5SHQ7) Pfam (PF00828)	Thermus thermophilus
38	GB, QC (CP, DP)	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252)	Thermus thermophilus
39	HB, RC (CQ, DQ)	50S ribosomal protein L17	polymer	117	13619.0	2	UniProt (Q9Z9H5) UniProt (Q72I33) Pfam (PF01196)	Thermus thermophilus
40	IB, SC (CR, DR)	50S ribosomal protein L18	polymer	98	10941.9	2	UniProt (Q5SHQ4) Pfam (PF00861)	Thermus thermophilus	TL24
41	JB, TC (CS, DS)	50S ribosomal protein L19	polymer	137	16218.8	2	UniProt (P60490) Pfam (PF01245)	Thermus thermophilus
42	KB, UC (CT, DT)	50S ribosomal protein L20	polymer	117	13572.0	2	UniProt (P60491) Pfam (PF00453)	Thermus thermophilus
43	LB, VC (CU, DU)	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829)	Thermus thermophilus
44	MB (CW)	50S ribosomal protein L22	polymer	113	12808.1	1	UniProt (Q5SHP3) Pfam (PF00237)	Thermus thermophilus
45	NB, XC (CX, DX)	50S ribosomal protein L23	polymer	92	10273.1	2	UniProt (Q5SHP0) Pfam (PF00276)	Thermus thermophilus
46	OB, YC (CY, DY)	50S ribosomal protein L24	polymer	100	11078.5	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136)	Thermus thermophilus
47	PB, ZC (CZ, DZ)	50S ribosomal protein L25	polymer	176	19892.9	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693)	Thermus thermophilus	TL5
48	AD, QB (Ca, Da)	50S ribosomal protein L27	polymer	84	9397.9	2	UniProt (P60493) Pfam (PF01016)	Thermus thermophilus
49	BD, RB (CH, DH)	50S ribosomal protein L28	polymer	93	10458.4	2	UniProt (Q72G84) UniProt (P60494) Pfam (PF00830)	Thermus thermophilus
50	CD, SB (CK, DK)	50S ribosomal protein L29	polymer	71	8539.1	2	UniProt (Q5SHP6) Pfam (PF00831)	Thermus thermophilus
51	DD, TB (CL, DL)	50S ribosomal protein L30	polymer	59	6670.0	2	UniProt (Q5SHQ6) Pfam (PF00327)	Thermus thermophilus
52	ED, UB (C5, D5)	50S ribosomal protein L31	polymer	30	3278.9	2	UniProt (Q5SJE1) Pfam (PF01197)	Thermus thermophilus
53	FD, VB (C6, D6)	50S ribosomal protein L32	polymer	59	6590.9	2	UniProt (P80339) Pfam (PF01783)	Thermus thermophilus
54	GD, WB (C7, D7)	50S ribosomal protein L33	polymer	44	5473.4	2	UniProt (P35871) Pfam (PF00471)	Thermus thermophilus
55	HD, XB (C8, D8)	50S ribosomal protein L34	polymer	48	5975.3	2	UniProt (P80340) Pfam (PF00468)	Thermus thermophilus
56	ID, YB (C9, D9)	50S ribosomal protein L35	polymer	63	7245.9	2	UniProt (Q5SKU1) Pfam (PF01632)	Thermus thermophilus
57	JD, ZB (C0, D0)	50S ribosomal protein L36	polymer	36	4304.2	2	UniProt (Q5SHR2) Pfam (PF00444)	Thermus thermophilus	Ribosomal protein B
58	AC, LD (C1, D1)	23S rRNA (2899-MER)	polymer	2899	942978.4	2		Thermus thermophilus
59	BC, KD (Cs, Ds)	5S rRNA (119-MER)	polymer	119	38553.0	2	GenBank (55771382)	Thermus thermophilus
60	CC (D2)	tRNA (5'-D(*AP*UP*CP*CP*CP*CP*GP*UP*GP*UP*CP*CP*UP*UP*GP*GP*UP*UP*CP*G)-3')	polymer	20	6289.7	1		Thermus thermophilus
61	EC (D4)	tRNA (76-MER)	polymer	76	24497.6	1		Thermus thermophilus
62	FC (DA)	50S ribosomal protein L1	polymer	206	19866.5	1	UniProt (Q5SLP7) Pfam (PF00687)	Thermus thermophilus
63	WC (DW)	50S ribosomal protein L22	polymer	113	12750.0	1	UniProt (Q5SHP3) Pfam (PF00237)	Thermus thermophilus
64	MD (DV)	DNA (55-MER)	polymer	55	17821.7	1		Thermus thermophilus
65	ND, OD (Ab, Bb)	PAROMOMYCIN	non-polymer		615.6	2	Chemie (PAR)
66	PD, RD (C1, D1)	Bactobolin A	non-polymer		381.3	2	Chemie (3V6)
67	QD, SD (C1, D1)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)

Sequence modifications

AI, BI: 2 - 128 (UniProt: P80374)

PDB	External Database	Details
Arg 58	His 58	conflict

Ab, Bb: 6 - 1509 (GenBank: 55771382)
CA: 18 - 110 (UniProt: Q5SLP7)

PDB	External Database	Details
Ala 106	Gly 107	conflict

CA: 119 - 233 (PDB: 4WT8)
CQ, DQ: 2 - 118 (UniProt: Q9Z9H5)
CT, DT: 2 - 118 (UniProt: P60491)

PDB	External Database	Details
Ala 32	Phe 32	conflict

CH, DH: 3 - 95 (UniProt: Q72G84)
Cs, Ds: 1 - 119 (PDB: 4WT8)
DA: 18 - 110 (UniProt: Q5SLP7)
DA: 119 - 233 (PDB: 4WT8)
DW: 1 - 112 (UniProt: Q5SHP3)

PDB	External Database	Details
Ala 113	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	117
	Total formula weight	4458654.7
Non-Polymers*	Number of molecules	6
	Total formula weight	2042.4
All*	Total formula weight	4460697.0

*Water molecules are not included.