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