6YSU

Structure of the P+0 ArfB-ribosome complex in the post-hydrolysis state

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	0	50S ribosomal protein L32	polymer	57	6463.4	1	UniProt (P0A7N4) Pfam (PF01783) In PDB	Escherichia coli	ribosomal protein bL32
2	1	50S ribosomal protein L33	polymer	55	6388.6	1	UniProt (P0A7N9) Pfam (PF00471) In PDB	Escherichia coli	ribosomal protein bL33
3	2	50S ribosomal protein L34	polymer	46	5397.5	1	UniProt (P0A7P5) Pfam (PF00468) In PDB	Escherichia coli	ribosomal protein bL34
4	3	50S ribosomal protein L35	polymer	65	7313.0	1	UniProt (P0A7Q1) Pfam (PF01632) In PDB	Escherichia coli	Ribosomal protein A,ribosomal protein bL35
5	4	50S ribosomal protein L36	polymer	38	4377.4	1	UniProt (P0A7Q6) Pfam (PF00444) In PDB	Escherichia coli	Ribosomal protein B,ribosomal protein bL36
6	5	50S ribosomal protein L10	polymer	165	17736.6	1	UniProt (A0A073UC57) In PDB	Escherichia coli
7	A	23S ribosomal RNA	polymer	2903	941518.4	1		Escherichia coli
8	B	5S ribosomal RNA	polymer	120	38790.1	1	GenBank (1726050194)	Escherichia coli
9	C	50S ribosomal protein L2	polymer	273	29923.6	1	UniProt (P60422) Pfam (PF00181) Pfam (PF03947) In PDB	Escherichia coli	ribosomal protein uL2
10	D	50S ribosomal protein L3	polymer	209	22277.5	1	UniProt (P60438) Pfam (PF00297) In PDB	Escherichia coli	ribosomal protein uL3
11	E	50S ribosomal protein L4	polymer	201	22121.6	1	UniProt (P60723) Pfam (PF00573) In PDB	Escherichia coli	ribosomal protein uL4
12	F	50S ribosomal protein L5	polymer	179	20333.6	1	UniProt (P62399) Pfam (PF00281) Pfam (PF00673) In PDB	Escherichia coli	ribosomal protein uL5
13	G	50S ribosomal protein L6	polymer	177	18932.8	1	UniProt (P0AG55) Pfam (PF00347) In PDB	Escherichia coli	ribosomal protein uL6
14	H	50S ribosomal protein L9	polymer	149	15789.0	1	UniProt (P0A7R1) Pfam (PF01281) Pfam (PF03948) In PDB	Escherichia coli	ribosomal protein bL9
15	I	50S ribosomal protein L11	polymer	142	14894.4	1	UniProt (P0A7J7) Pfam (PF03946) Pfam (PF00298) In PDB	Escherichia coli	ribosomal protein uL11
16	J	50S ribosomal protein L13	polymer	142	16050.6	1	UniProt (P0AA10) Pfam (PF00572) In PDB	Escherichia coli	ribosomal protein uL13
17	K	50S ribosomal protein L14	polymer	123	13565.1	1	UniProt (P0ADY3) Pfam (PF00238) In PDB	Escherichia coli	ribosomal protein uL14
18	L	50S ribosomal protein L15	polymer	144	15008.5	1	UniProt (P02413) Pfam (PF00828) In PDB	Escherichia coli	ribosomal protein uL15
19	M	50S ribosomal protein L16	polymer	136	15312.3	1	UniProt (P0ADY7) Pfam (PF00252) In PDB	Escherichia coli	ribosomal protein uL16
20	N	50S ribosomal protein L17	polymer	127	14393.7	1	UniProt (P0AG44) Pfam (PF01196) In PDB	Escherichia coli	ribosomal protein uL17
21	O	50S ribosomal protein L18	polymer	117	12794.7	1	UniProt (P0C018) Pfam (PF00861) In PDB	Escherichia coli	ribosomal protein uL18
22	P	50S ribosomal protein L19	polymer	115	13159.3	1	UniProt (P0A7K6) Pfam (PF01245) In PDB	Escherichia coli	ribosomal protein bL19
23	Q	50S ribosomal protein L20	polymer	118	13528.0	1	UniProt (P0A7L3) Pfam (PF00453) In PDB	Escherichia coli	ribosomal protein bL20
24	R	50S ribosomal protein L21	polymer	103	11586.4	1	UniProt (P0AG48) Pfam (PF00829) In PDB	Escherichia coli	ribosomal protein bL21
25	S	50S ribosomal protein L22	polymer	110	12253.4	1	UniProt (P61175) Pfam (PF00237) In PDB	Escherichia coli	ribosomal protein uL22
26	T	50S ribosomal protein L23	polymer	100	11222.2	1	UniProt (P0ADZ0) Pfam (PF00276) In PDB	Escherichia coli	ribosomal protein uL23
27	U	50S ribosomal protein L24	polymer	104	11339.3	1	UniProt (P60624) Pfam (PF00467) Pfam (PF17136) In PDB	Escherichia coli	ribosomal protein uL24
28	V	50S ribosomal protein L25	polymer	94	10713.5	1	UniProt (P68919) Pfam (PF01386) In PDB	Escherichia coli	ribosomal protein bL25
29	W	50S ribosomal protein L27	polymer	85	9146.5	1	UniProt (P0A7L8) Pfam (PF01016) In PDB	Escherichia coli	ribosomal protein bL27
30	X	50S ribosomal protein L28	polymer	78	9027.6	1	UniProt (P0A7M2) Pfam (PF00830) In PDB	Escherichia coli	ribosomal protein bL28
31	Y	50S ribosomal protein L29	polymer	63	7286.5	1	UniProt (P0A7M6) Pfam (PF00831) In PDB	Escherichia coli	ribosomal protein uL29
32	Z	50S ribosomal protein L30	polymer	59	6554.8	1	UniProt (P0AG51) Pfam (PF00327) In PDB	Escherichia coli	ribosomal protein uL30
33	a	16S ribosomal RNA	polymer	1542	499873.4	1		Escherichia coli
34	b	30S ribosomal protein S2	polymer	240	26652.6	1	UniProt (C3TPN2) Pfam (PF00318) In PDB	Escherichia coli
35	c	30S ribosomal protein S3	polymer	233	26031.3	1	UniProt (C3SQX2) Pfam (PF07650) Pfam (PF00189) In PDB	Escherichia coli
36	d	30S ribosomal protein S4	polymer	206	23514.2	1	UniProt (C3SR62) Pfam (PF00163) Pfam (PF01479) In PDB	Escherichia coli
37	e	30S ribosomal protein S5	polymer	167	17629.4	1	UniProt (C3SR27) Pfam (PF00333) Pfam (PF03719) In PDB	Escherichia coli
38	f	30S ribosomal protein S6	polymer	135	15727.5	1		Escherichia coli
39	g	30S ribosomal protein S7	polymer	179	20055.2	1	UniProt (A0A5Q2GFB5) In PDB	Escherichia coli
40	h	30S ribosomal protein S8	polymer	130	14146.6	1	UniProt (C3SR12) Pfam (PF00410) In PDB	Escherichia coli
41	i	30S ribosomal protein S9	polymer	130	14886.3	1	UniProt (C3SRY2) Pfam (PF00380) In PDB	Escherichia coli
42	j	30S ribosomal protein S10	polymer	103	11755.6	1	UniProt (C3SQT7) Pfam (PF00338) In PDB	Escherichia coli
43	k	30S ribosomal protein S11	polymer	129	13871.0	1	UniProt (C3SR57) Pfam (PF00411) In PDB	Escherichia coli
44	l	30S ribosomal protein S12	polymer	124	13768.2	1	UniProt (C3SQR7) Pfam (PF00164) In PDB	Escherichia coli
45	m	30S ribosomal protein S13	polymer	118	13128.5	1	UniProt (C3SR52) Pfam (PF00416) In PDB	Escherichia coli
46	n	30S ribosomal protein S14	polymer	102	11677.6	1	UniProt (C3SR07) Pfam (PF00253) In PDB	Escherichia coli
47	o	30S ribosomal protein S15	polymer	89	10290.8	1	UniProt (C3SSQ7) Pfam (PF00312) In PDB	Escherichia coli
48	p	30S ribosomal protein S16	polymer	82	9207.6	1	UniProt (C3SYP2) Pfam (PF00886) In PDB	Escherichia coli
49	q	30S ribosomal protein S17	polymer	84	9724.5	1	UniProt (C3SQY7) Pfam (PF00366) In PDB	Escherichia coli
50	r	30S ribosomal protein S18	polymer	75	9005.5	1	UniProt (C3SFP7) Pfam (PF01084) In PDB	Escherichia coli
51	s	30S ribosomal protein S19	polymer	92	10455.4	1	UniProt (C3SQW2) Pfam (PF00203) In PDB	Escherichia coli
52	t	30S ribosomal protein S20	polymer	87	9708.5	1	UniProt (C3TRH7) Pfam (PF01649) In PDB	Escherichia coli
53	u	30S ribosomal protein S21	polymer	71	8524.0	1	UniProt (C3STZ7) Pfam (PF01165) In PDB	Escherichia coli
54	v	Api137	polymer	14	1699.1	1	UniProt (Q8WSY8) Pfam (PF00807) In PDB	Apis mellifera	Apidaescin
55	w	P-site tRNAPhe	polymer	76	24643.9	1		Escherichia coli
56	x	RNA (5'-R(P*AP*UP*GP*UP*UP*C)-3')	polymer	15	4716.8	1		Escherichia coli
57	y	Alternative stalled-ribosome rescue factor B	polymer	140	15656.1	1	UniProt (A0A024L8R9) Pfam (PF00472) In PDB	Escherichia coli	Aminoacyl-tRNA hydrolase,Class I peptide chain release factor,Peptidyl-tRNA hydrolase ArfB,Peptidyl-tRNA hydrolase YaeJ,Protein YaeJ,Putative peptidyl-tRNA hydrolase
58	A, C, a, D, L...	MAGNESIUM ION	non-polymer		24.3	356	Chemie (MG)
59	4	ZINC ION	non-polymer		65.4	1	Chemie (ZN)
60	A	SODIUM ION	non-polymer		23.0	1	Chemie (NA)

Sequence modifications

n: 0 - 101 (UniProt: C3SR07)

PDB	External Database	Details
Ala 35	-	insertion

v: 5 - 18 (UniProt: Q8WSY8)

PDB	External Database	Details
Arg 10	Gln 23	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	57
	Total formula weight	2211548.8
Non-Polymers*	Number of molecules	358
	Total formula weight	8741.0
All*	Total formula weight	2220289.8

*Water molecules are not included.