9NJF

E. coli pre-elongation complex without an A-site tRNA with EQ2-YbiT in Non-hydrolytic 1/PtIM(a) conformation

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 (1)	Large ribosomal subunit protein uL1	polymer	220	23392.1	1	UniProt (P0A7L0) Pfam (PF00687)	Escherichia coli	50S ribosomal protein L1
2	B (10)	Large ribosomal subunit protein uL10	polymer	131	14112.3	1	UniProt (P0A7J3) Pfam (PF00466)	Escherichia coli	50S ribosomal protein L10,50S ribosomal protein L8
3	C (11)	Large ribosomal subunit protein uL11	polymer	141	14763.2	1	UniProt (P0A7J7) Pfam (PF03946) Pfam (PF00298)	Escherichia coli	50S ribosomal protein L11
4	D (13)	Large ribosomal subunit protein uL13	polymer	142	16050.6	1	UniProt (P0AA10) Pfam (PF00572)	Escherichia coli	50S ribosomal protein L13
5	E (14)	Large ribosomal subunit protein uL14	polymer	123	13565.1	1	UniProt (P0ADY3) Pfam (PF00238)	Escherichia coli	50S ribosomal protein L14
6	F (15)	50S ribosomal protein L15	polymer	143	14877.3	1	UniProt (A0A037Y8L6) Pfam (PF00828) UniProt (by SIFTS) (P02413)	Escherichia coli
7	G (16)	50S ribosomal protein L16	polymer	136	15312.3	1	UniProt (P0ADY7) Pfam (PF00252)	Escherichia coli	Large ribosomal subunit protein uL16
8	H (17)	Large ribosomal subunit protein bL17	polymer	120	13721.9	1	UniProt (P0AG44) Pfam (PF01196)	Escherichia coli	50S ribosomal protein L17
9	I (18)	Large ribosomal subunit protein uL18	polymer	116	12663.5	1	UniProt (P0C018) Pfam (PF00861)	Escherichia coli	50S ribosomal protein L18
10	J (19)	50S ribosomal protein L19	polymer	114	13028.1	1	UniProt (S1PSA3) Pfam (PF01245) UniProt (by SIFTS) (P0A7K6)	Escherichia coli
11	K (2)	50S ribosomal protein L2	polymer	271	29663.2	1	UniProt (P60422) Pfam (PF00181) Pfam (PF03947)	Escherichia coli	Large ribosomal subunit protein uL2
12	L (20)	Large ribosomal subunit protein bL20	polymer	117	13396.8	1	UniProt (C3T7Q7)	Escherichia coli
13	M (21)	Large ribosomal subunit protein bL21	polymer	103	11586.4	1	UniProt (Q1R6F0) Pfam (PF00829) UniProt (by SIFTS) (P0AG48)	Escherichia coli	50S ribosomal protein L21
14	N (22)	Large ribosomal subunit protein uL22	polymer	110	12253.4	1	UniProt (Q1R610) Pfam (PF00237) UniProt (by SIFTS) (P61175)	Escherichia coli	50S ribosomal protein L22
15	O (23)	Large ribosomal subunit protein uL23	polymer	93	10546.5	1	UniProt (C3SQV2) Pfam (PF00276) UniProt (by SIFTS) (P0ADZ0)	Escherichia coli
16	P (24)	Large ribosomal subunit protein uL24	polymer	102	11078.9	1	UniProt (A0A7U9LWC1) Pfam (PF00467) Pfam (PF17136) UniProt (by SIFTS) (P60624)	Escherichia coli	50S ribosomal protein L24
17	Q (25)	Large ribosomal subunit protein bL25	polymer	94	10713.5	1	UniProt (P68919) Pfam (PF01386)	Escherichia coli
18	R (27)	50S ribosomal protein L27	polymer	75	8174.4	1	UniProt (A0A1X3JCC7) Pfam (PF01016) UniProt (by SIFTS) (P0A7L8)	Escherichia coli
19	S (28)	50S ribosomal protein L28	polymer	77	8896.4	1	UniProt (A0A0E2KZD0) Pfam (PF00830) UniProt (by SIFTS) (P0A7M2)	Escherichia coli
20	T (29)	Large ribosomal subunit protein uL29	polymer	63	7286.5	1	UniProt (C3SQY2) Pfam (PF00831) UniProt (by SIFTS) (P0A7M6)	Escherichia coli
21	U (3)	50S ribosomal protein L3	polymer	209	22277.5	1	UniProt (P60438) Pfam (PF00297)	Escherichia coli	Large ribosomal subunit protein uL3
22	V (30)	50S ribosomal protein L30	polymer	58	6423.6	1	UniProt (P0AG51) Pfam (PF00327)	Escherichia coli	Large ribosomal subunit protein uL30
23	W (31)	Large ribosomal subunit protein bL31	polymer	66	7516.7	1	UniProt (P0A7M9) Pfam (PF01197)	Escherichia coli	50S ribosomal protein L31
24	X (32)	50S ribosomal protein L32	polymer	56	6332.2	1	UniProt (A0A828UBL8) Pfam (PF01783) UniProt (by SIFTS) (P0A7N4)	Escherichia coli
25	Y (33)	Large ribosomal subunit protein bL33	polymer	50	5814.8	1	UniProt (P0A7N9) Pfam (PF00471)	Escherichia coli	50S ribosomal protein L33
26	Z (34)	50S ribosomal protein L34	polymer	46	5397.5	1	UniProt (B7MGC4) Pfam (PF00468) UniProt (by SIFTS) (P0A7P5)	Escherichia coli
27	AA (35)	Large ribosomal subunit protein bL35	polymer	64	7181.8	1	UniProt (P0A7Q2) Pfam (PF01632) UniProt (by SIFTS) (P0A7Q1)	Escherichia coli
28	BA (36)	50S ribosomal protein L36	polymer	38	4377.4	1	UniProt (A0A0E2L017) Pfam (PF00444) UniProt (by SIFTS) (P0A7Q6)	Escherichia coli
29	CA (4)	Large ribosomal subunit protein uL4	polymer	201	22121.6	1	UniProt (P60723) Pfam (PF00573)	Escherichia coli	50S ribosomal protein L4
30	DA (5)	50S ribosomal protein L5	polymer	177	20073.2	1	UniProt (A0A4P8BX24) Pfam (PF00281) Pfam (PF00673) UniProt (by SIFTS) (P62399)	Escherichia coli
31	EA (6)	Large ribosomal subunit protein uL6	polymer	176	18801.6	1	UniProt (C3SR17) Pfam (PF00347) UniProt (by SIFTS) (P0AG55)	Escherichia coli
32	FA (9)	Large ribosomal subunit protein bL9	polymer	149	15789.0	1	UniProt (P0A7R1) Pfam (PF01281) Pfam (PF03948)	Escherichia coli	50S ribosomal protein L9
33	GA (M)	mRNA	polymer	6	1900.2	1		Escherichia coli
34	HA (R1)	23S ribosomal RNA	polymer	2903	941322.2	1	GenBank (2019144442)	Escherichia coli
35	IA (R2)	5S ribosomal RNA	polymer	119	38483.9	1	GenBank (1815787944)	Escherichia coli
36	JA (R3)	16S ribosomal RNA	polymer	1538	498420.2	1	GenBank (2044032419)	Escherichia coli
37	KA (T)	tRNA	polymer	76	24506.6	1	GenBank (1845258627)	Escherichia coli
38	LA (Y)	Probable ATP-binding protein YbiT	polymer	530	59924.9	1	UniProt (P0A9U3) Pfam (PF00005) Pfam (PF12848)	Escherichia coli
39	MA (sb)	Small ribosomal subunit protein uS2	polymer	218	24253.9	1	UniProt (P0A7V0) Pfam (PF00318)	Escherichia coli	30S ribosomal protein S2
40	NA (sc)	Small ribosomal subunit protein uS3	polymer	206	23078.8	1	UniProt (P0A7V5) Pfam (PF07650) Pfam (PF00189) UniProt (by SIFTS) (P0A7V3)	Escherichia coli	30S ribosomal protein S3
41	OA (sd)	30S ribosomal protein S4	polymer	205	23383.0	1	UniProt (C3SR62) Pfam (PF00163) Pfam (PF01479) UniProt (by SIFTS) (P0A7V8)	Escherichia coli
42	PA (se)	Small ribosomal subunit protein uS5	polymer	157	16532.1	1	UniProt (P0A7W1) Pfam (PF00333) Pfam (PF03719)	Escherichia coli	30S ribosomal protein S5
43	QA (sf)	30S ribosomal protein S6, non-modified isoform	polymer	100	11669.4	1	UniProt (P02358) Pfam (PF01250)	Escherichia coli
44	RA (sg)	30S ribosomal protein S7	polymer	151	16861.5	1	UniProt (P02359) Pfam (PF00177)	Escherichia coli	Small ribosomal subunit protein uS7
45	SA (sh)	30S ribosomal protein S8	polymer	129	14015.4	1	UniProt (A0A828U358) Pfam (PF00410) UniProt (by SIFTS) (P0A7W7)	Escherichia coli
46	TA (si)	Small ribosomal subunit protein uS9	polymer	127	14554.9	1	UniProt (C3SRY2) Pfam (PF00380) UniProt (by SIFTS) (P0A7X3)	Escherichia coli
47	UA (sj)	30S ribosomal protein S10	polymer	98	11197.0	1	UniProt (A0A0H3EQD3) Pfam (PF00338) UniProt (by SIFTS) (P0A7R5)	Escherichia coli
48	VA (sk)	Small ribosomal subunit protein uS11	polymer	116	12388.1	1	UniProt (C3SR57) Pfam (PF00411) UniProt (by SIFTS) (P0A7R9)	Escherichia coli
49	WA (sl)	Small ribosomal subunit protein uS12	polymer	123	13637.0	1	UniProt (C3SQR7) Pfam (PF00164) UniProt (by SIFTS) (P0A7S3)	Escherichia coli
50	XA (sm)	30S ribosomal protein S13	polymer	114	12625.8	1	UniProt (S1P5F8) Pfam (PF00416) UniProt (by SIFTS) (P0A7S9)	Escherichia coli
51	YA (sn)	Small ribosomal subunit protein uS14	polymer	100	11475.4	1	UniProt (A0A8S0FJJ0) Pfam (PF00253) UniProt (by SIFTS) (P0AG59)	Escherichia coli
52	ZA (so)	Small ribosomal subunit protein uS15	polymer	88	10159.6	1	UniProt (P0ADZ4) Pfam (PF00312)	Escherichia coli	30S ribosomal protein S15
53	AB (sp)	Small ribosomal subunit protein bS16	polymer	82	9207.6	1	UniProt (C3SYP2) Pfam (PF00886) UniProt (by SIFTS) (P0A7T3)	Escherichia coli
54	BB (sq)	Small ribosomal subunit protein uS17	polymer	80	9263.9	1	UniProt (P0AG63) Pfam (PF00366)	Escherichia coli	30S ribosomal protein S17
55	CB (sr)	30S ribosomal protein S18	polymer	65	7606.8	1	UniProt (E0J6I2) Pfam (PF01084) UniProt (by SIFTS) (P0A7T7)	Escherichia coli
56	DB (ss)	30S ribosomal protein S19	polymer	79	9057.6	1	UniProt (A0A7U9LGZ0) Pfam (PF00203) UniProt (by SIFTS) (P0A7U3)	Escherichia coli
57	EB (st)	30S ribosomal protein S20	polymer	85	9506.2	1	UniProt (C3TRH7) Pfam (PF01649) UniProt (by SIFTS) (P0A7U7)	Escherichia coli
58	FB (su)	Small ribosomal subunit protein bS21	polymer	65	7763.1	1	UniProt (P68679) Pfam (PF01165)	Escherichia coli	30S ribosomal protein S21
59	AC, AD, AE, AF, AG... (R1, R3, 18, 32, 33...)	MAGNESIUM ION	non-polymer		24.3	124	Chemie (MG)
60	JB (36)	ZINC ION	non-polymer		65.4	1	Chemie (ZN)
61	BG, CG (Y)	ADENOSINE-5'-TRIPHOSPHATE	non-polymer		507.2	2	Chemie (ATP)
62	DG, EG (Y)	SODIUM ION	non-polymer		23.0	2	Chemie (NA)

Sequence modifications

R1: 1 - 2903 (GenBank: 2019144442)

PDB	External Database	Details
G 1847	A 2609611	conflict

T: 1 - 76 (GenBank: 1845258627)

PDB	External Database	Details
A 34	U 666844	conflict

Y: 1 - 530 (UniProt: P0A9U3)

PDB	External Database	Details
Gln 181	Glu 181	conflict
Gln 464	Glu 464	conflict

Contents of the asymmetric unit

Polymers	Number of chains	58
	Total formula weight	2249984.0
Non-Polymers*	Number of molecules	129
	Total formula weight	4139.6
All*	Total formula weight	2254123.6

*Water molecules are not included.