5NDJ

Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)

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	13, 1G	16S ribosomal RNA	polymer	1522	493997.3	2	GenBank (55771382)	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
2	A8, 65	50S ribosomal protein L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	TL24
3	B5, F8	50S ribosomal protein L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
4	11, 19	50S ribosomal protein L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF03947) Pfam (PF00181) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
5	L5, P8	50S ribosomal protein L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
6	2A, 2I	30S ribosomal protein S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
7	8I, 8A	30S ribosomal protein S17	polymer	105	12325.7	2	UniProt (Q5SHP7) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
8	22, 2E	30S ribosomal protein S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
9	8E, 82	30S ribosomal protein S9	polymer	128	14410.6	2	UniProt (P80374) Pfam (PF00380) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
10	58, 15	50S ribosomal protein L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
11	G8, C5	50S ribosomal protein L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
12	Q8, M5	50S ribosomal protein L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
13	3I, 3A	30S ribosomal protein S12	polymer	132	14637.4	2	UniProt (Q5SHN3) Pfam (PF00164) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
14	3E, 32	30S ribosomal protein S4	polymer	209	24373.4	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
15	1H, 14	23S ribosomal RNA	polymer	2917	948539.9	2	GenBank (55771382)	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
16	B8, 75	50S ribosomal protein L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
17	L8, H5	50S ribosomal protein L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
18	61, 69	50S ribosomal protein L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
19	9I, 9A	30S ribosomal protein S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
20	1F, 1B	30S ribosomal protein Thx	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	S31
21	68, 25	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
22	H8, D5	50S ribosomal protein L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	TL5
23	21, 29	50S ribosomal protein L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
24	4I, 4A	30S ribosomal protein S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
25	4E, 42	30S ribosomal protein S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
26	16, 1J	5S ribosomal RNA	polymer	122	39540.6	2	GenBank (55771382)	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
27	C8, 85	50S ribosomal protein L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
28	M8, I5	50S ribosomal protein L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
29	AI, AA	30S ribosomal protein S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
30	78, 35	50S ribosomal protein L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
31	I8, E5	50S ribosomal protein L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
32	31, 39	50S ribosomal protein L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	L1e
33	5I, 5A	30S ribosomal protein S14 type Z	polymer	61	7158.7	2	UniProt (Q5SHQ1) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
34	5E, 52	30S ribosomal protein S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	TS9
35	D8, 95	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
36	N8, J5	50S ribosomal protein L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
37	BI, BA	30S ribosomal protein S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
38	88, 45	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
39	J8, F5	50S ribosomal protein L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
40	41, 49	50S ribosomal protein L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
41	6I, 6A	30S ribosomal protein S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
42	6E, 62	30S ribosomal protein S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
43	E8, A5	50S ribosomal protein L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
44	1E, 12	30S ribosomal protein S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
45	98, 55	50S ribosomal protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
46	K8, G5	50S ribosomal protein L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
47	51, 59	50S ribosomal protein L6	polymer	180	19568.9	2	UniProt (Q5SHQ3) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
48	1A, 1I	30S ribosomal protein S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
49	7I, 7A	30S ribosomal protein S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
50	7E, 72	30S ribosomal protein S8	polymer	138	15868.6	2	UniProt (Q5SHQ2) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
51	Y1, Y4	mRNA	polymer	25	7911.6	2		Escherichia coli
52	W1, X1, V1, W4, X4...	tRNA-Phe	polymer	76	24485.5	6	GenBank (1134491115)	Escherichia coli
53	1G, 13, 14, 1H	TC007	non-polymer		483.5	13	Chemie (8UZ)
54	1H, 14, 13, 11, 1G...	MAGNESIUM ION	non-polymer		24.3	1770	Chemie (MG)
55	5A, C5, 32, G8, 5I...	ZINC ION	non-polymer		65.4	6	Chemie (ZN)
56		water	water		18.0	1241	Chemie (HOH)

Sequence modifications

13, 1G: 646 - 2167 (GenBank: 55771382)

PDB	External Database	Details
G 2165	U 132819	conflict

1H, 14: 1 - 2919 (GenBank: 55771382)

PDB	External Database	Details
U 156	Unk 9395	conflict
A 682	G 9920	conflict
C 686	G 9924	conflict
G 697	C 9935	conflict
A 701	C 9939	conflict
U 1106	G 10344	conflict
A 1128	C 10366	conflict

Contents of the asymmetric unit

Polymers	Number of chains	108
	Total formula weight	4479474.8
Non-Polymers*	Number of molecules	1789
	Total formula weight	49698.0
All*	Total formula weight	4529172.8

*Water molecules are not included.