4V5K

Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome

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	AA, CA	16S ribosomal RNA	polymer	1522	494038.3	2	GenBank (55979969)	Thermus thermophilus HB8
2	AB, CB	30S RIBOSOMAL PROTEIN S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318) In PDB	Thermus thermophilus HB8
3	AC, CC	30S RIBOSOMAL PROTEIN S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189) In PDB	Thermus thermophilus HB8
4	AD, CD	30S RIBOSOMAL PROTEIN S4	polymer	209	24373.4	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479) In PDB	Thermus thermophilus HB8
5	AE, CE	30S RIBOSOMAL PROTEIN S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719) In PDB	Thermus thermophilus HB8
6	AF, CF	30S RIBOSOMAL PROTEIN S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250) In PDB	Thermus thermophilus HB8	TS9
7	AG, CG	30S RIBOSOMAL PROTEIN S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177) In PDB	Thermus thermophilus HB8
8	AH, CH	30S RIBOSOMAL PROTEIN S8	polymer	138	15868.6	2	UniProt (Q5SHQ2) In PDB	Thermus thermophilus HB8
9	AI, CI	30S RIBOSOMAL PROTEIN S9	polymer	128	14429.7	2	UniProt (P80374) UniProt (P62669) Pfam (PF00380) In PDB	Thermus thermophilus HB8
10	AJ, CJ	30S RIBOSOMAL PROTEIN S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338) In PDB	Thermus thermophilus HB8
11	AK, CK	30S RIBOSOMAL PROTEIN S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411) In PDB	Thermus thermophilus HB8
12	AL, CL	30S RIBOSOMAL PROTEIN S12	polymer	135	14920.8	2	UniProt (Q5SHN3) Pfam (PF00164) In PDB	Thermus thermophilus HB8
13	AM, CM	30S RIBOSOMAL PROTEIN S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416) In PDB	Thermus thermophilus HB8
14	AN, CN	30S RIBOSOMAL PROTEIN S14 TYPE Z	polymer	61	7158.7	2	UniProt (Q5SHQ1) In PDB	Thermus thermophilus HB8	30S RIBOSOMAL PROTEIN S14
15	AO, CO	30S RIBOSOMAL PROTEIN S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312) In PDB	Thermus thermophilus HB8
16	AP, CP	30S RIBOSOMAL PROTEIN S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886) In PDB	Thermus thermophilus HB8
17	AQ, CQ	30S RIBOSOMAL PROTEIN S17	polymer	105	12325.7	2	UniProt (Q5SHP7) In PDB	Thermus thermophilus HB8
18	AR, CR	30S RIBOSOMAL PROTEIN S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084) In PDB	Thermus thermophilus HB8
19	AS, CS	30S RIBOSOMAL PROTEIN S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203) In PDB	Thermus thermophilus HB8
20	AT, CT	30S RIBOSOMAL PROTEIN S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649) In PDB	Thermus thermophilus HB8
21	AU, CU	30S RIBOSOMAL PROTEIN THX	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070) In PDB	Thermus thermophilus HB8	S31
22	AV, AW, CV, CW	E-SITE TRNA PHE OR P-SITE TRNA PHE	polymer	77	24802.8	4		Escherichia coli K-12
23	AX	MRNA	polymer	25	8157.0	1		synthetic construct
24	AY, CY	COLICIN-E3	polymer	97	10874.2	2	UniProt (P00646) Pfam (PF09000) In PDB	Escherichia coli	COLICIN-E3 A CHAIN, RIBONUCLEASE
25	B0, D0	50S RIBOSOMAL PROTEIN L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016) In PDB	Thermus thermophilus HB8
26	B1, D1	50S RIBOSOMAL PROTEIN L28	polymer	98	11032.2	2	UniProt (P60494) Pfam (PF00830) In PDB	Thermus thermophilus HB8
27	B2, D2	50S RIBOSOMAL PROTEIN L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831) In PDB	Thermus thermophilus HB8
28	B3, D3	50S RIBOSOMAL PROTEIN L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327) In PDB	Thermus thermophilus HB8
29	B4, D4	50S RIBOSOMAL PROTEIN L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197) In PDB	Thermus thermophilus HB8
30	B5, D5	50S RIBOSOMAL PROTEIN L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783) In PDB	Thermus thermophilus HB8
31	B6, D6	50S RIBOSOMAL PROTEIN L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471) In PDB	Thermus thermophilus HB8
32	B7, D7	50S RIBOSOMAL PROTEIN L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468) In PDB	Thermus thermophilus HB8
33	B8, D8	50S RIBOSOMAL PROTEIN L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632) In PDB	Thermus thermophilus HB8
34	B9, D9	50S RIBOSOMAL PROTEIN L36	polymer	37	4435.4	2	UniProt (Q5SHR2) Pfam (PF00444) In PDB	Thermus thermophilus HB8	RIBOSOMAL PROTEIN B
35	BA, DA	23S ribosomal RNA	polymer	2848	926365.8	2		Thermus thermophilus HB8
36	BB, DB	5S ribosomal RNA	polymer	122	39494.5	2	GenBank (55979969)	Thermus thermophilus HB8
37	BC, DC	50S RIBOSOMAL PROTEIN L1	polymer	229	24872.7	2	UniProt (Q5SLP7) Pfam (PF00687) In PDB	Thermus thermophilus HB8
38	BD, DD	50S RIBOSOMAL PROTEIN L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947) In PDB	Thermus thermophilus HB8
39	BE, DE	50S RIBOSOMAL PROTEIN L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297) In PDB	Thermus thermophilus HB8
40	BF, DF	50S RIBOSOMAL PROTEIN L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573) In PDB	Thermus thermophilus HB8	L1E
41	BG, DG	50S RIBOSOMAL PROTEIN L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673) In PDB	Thermus thermophilus HB8
42	BH, DH	50S RIBOSOMAL PROTEIN L6	polymer	180	19568.9	2	UniProt (Q5SHQ3) In PDB	Thermus thermophilus HB8
43	BI, DI	50S RIBOSOMAL PROTEIN L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948) In PDB	Thermus thermophilus HB8
44	BJ, DJ	50S RIBOSOMAL PROTEIN L10	polymer	131	11166.8	2		Thermus thermophilus HB8
45	BN, DN	50S RIBOSOMAL PROTEIN L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572) In PDB	Thermus thermophilus HB8
46	BO, DO	50S RIBOSOMAL PROTEIN L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238) In PDB	Thermus thermophilus HB8
47	BP, DP	50S RIBOSOMAL PROTEIN L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828) In PDB	Thermus thermophilus HB8
48	BQ, DQ	50S RIBOSOMAL PROTEIN L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252) In PDB	Thermus thermophilus HB8
49	BR, DR	50S RIBOSOMAL PROTEIN L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196) In PDB	Thermus thermophilus HB8
50	BS, DS	50S RIBOSOMAL PROTEIN L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861) In PDB	Thermus thermophilus HB8	TL24
51	BT, DT	50S RIBOSOMAL PROTEIN L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245) In PDB	Thermus thermophilus HB8
52	BU, DU	50S RIBOSOMAL PROTEIN L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453) In PDB	Thermus thermophilus HB8
53	BV, DV	50S RIBOSOMAL PROTEIN L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829) In PDB	Thermus thermophilus HB8
54	BW, DW	50S RIBOSOMAL PROTEIN L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237) In PDB	Thermus thermophilus HB8
55	BX, DX	50S RIBOSOMAL PROTEIN L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276) In PDB	Thermus thermophilus HB8
56	BY, DY	50S RIBOSOMAL PROTEIN L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136) In PDB	Thermus thermophilus HB8
57	BZ, DZ	50S RIBOSOMAL PROTEIN L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693) In PDB	Thermus thermophilus HB8	TL5
58	CX	MRNA	polymer	25	8196.0	1		synthetic construct
59	BA, CA, DA, AA, CV...	MAGNESIUM ION	non-polymer		24.3	2334	Chemie (MG)
60	AD, AN, CD	ZINC ION	non-polymer		65.4	4	Chemie (ZN)
61		water	water		18.0	2	Chemie (HOH)

Sequence modifications

AI, CI: 1 - 128 (UniProt: P62669)
AY, CY: 0 - 96 (UniProt: P00646)

PDB	External Database	Details
Ala 58	His 45	engineered mutation

B1, D1: 1 - 98 (UniProt: P60494)

PDB	External Database	Details
Arg 81	Lys 81	conflict

Contents of the asymmetric unit

Polymers	Number of chains	116
	Total formula weight	4504569.1
Non-Polymers*	Number of molecules	2338
	Total formula weight	56989.5
All*	Total formula weight	4561558.6

*Water molecules are not included.