5FDV

Crystal structure of the Pyrrhocoricin antimicrobial peptide bound to the Thermus thermophilus 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	1A, 2A	23S ribosomal RNA	polymer	2915	948007.6	2	GenBank (55771382)	Thermus thermophilus HB8
2	1B, 2B	5S ribosomal RNA	polymer	120	38882.2	2	GenBank (55771382)	Thermus thermophilus HB8
3	1D, 2D	50S ribosomal protein L2	polymer	275	30401.4	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947) In PDB	Thermus thermophilus HB8
4	1E, 2E	50S ribosomal protein L3	polymer	204	22250.0	2	UniProt (Q5SHN8) Pfam (PF00297) In PDB	Thermus thermophilus HB8
5	1F, 2F	50S ribosomal protein L4	polymer	203	22512.0	2	UniProt (Q5SHN9) Pfam (PF00573) In PDB	Thermus thermophilus HB8	L1e
6	1G, 2G	50S ribosomal protein L5	polymer	181	20930.4	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673) In PDB	Thermus thermophilus HB8
7	1H, 2H	50S ribosomal protein L6	polymer	174	18980.2	2	UniProt (Q5SHQ3) In PDB	Thermus thermophilus HB8
8	1I, 2I	50S ribosomal protein L9	polymer	147	16293.1	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948) In PDB	Thermus thermophilus HB8
9	1N, 2N	50S ribosomal protein L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572) In PDB	Thermus thermophilus HB8
10	1O, 2O	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238) In PDB	Thermus thermophilus HB8
11	1P, 2P	50S ribosomal protein L15	polymer	149	16248.1	2	UniProt (Q5SHQ7) Pfam (PF00828) In PDB	Thermus thermophilus HB8
12	1Q, 2Q	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252) In PDB	Thermus thermophilus HB8
13	1R, 2R	50S ribosomal protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196) In PDB	Thermus thermophilus HB8
14	1S, 2S	50S ribosomal protein L18	polymer	110	12437.6	2	UniProt (Q5SHQ4) Pfam (PF00861) In PDB	Thermus thermophilus HB8	TL24
15	1T, 2T	50S ribosomal protein L19	polymer	131	15503.0	2	UniProt (P60490) Pfam (PF01245) In PDB	Thermus thermophilus HB8
16	1U, 2U	50S ribosomal protein L20	polymer	116	13591.0	2	UniProt (P60491) Pfam (PF00453) In PDB	Thermus thermophilus HB8
17	1V, 2V	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829) In PDB	Thermus thermophilus HB8
18	1W, 2W	50S ribosomal protein L22	polymer	112	12678.9	2	UniProt (Q5SHP3) Pfam (PF00237) In PDB	Thermus thermophilus HB8
19	1X, 2X	50S ribosomal protein L23	polymer	95	10646.6	2	UniProt (Q5SHP0) Pfam (PF00276) In PDB	Thermus thermophilus HB8
20	1Y, 2Y	50S ribosomal protein L24	polymer	107	11726.3	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136) In PDB	Thermus thermophilus HB8
21	1Z, 2Z	50S ribosomal protein L25	polymer	203	22851.2	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693) In PDB	Thermus thermophilus HB8	TL5
22	10, 20	50S ribosomal protein L27	polymer	77	8689.0	2	UniProt (P60493) Pfam (PF01016) In PDB	Thermus thermophilus HB8
23	11, 21	50S ribosomal protein L28	polymer	97	10873.0	2	UniProt (P60494) Pfam (PF00830) In PDB	Thermus thermophilus HB8
24	12, 22	50S ribosomal protein L29	polymer	70	8485.1	2	UniProt (Q5SHP6) Pfam (PF00831) In PDB	Thermus thermophilus HB8
25	13, 23	50S ribosomal protein L30	polymer	59	6667.9	2	UniProt (Q5SHQ6) Pfam (PF00327) In PDB	Thermus thermophilus HB8
26	14, 24	50S ribosomal protein L31	polymer	69	8086.3	2	UniProt (Q5SJE1) Pfam (PF01197) In PDB	Thermus thermophilus HB8
27	15, 25	50S ribosomal protein L32	polymer	59	6590.9	2	UniProt (P80339) Pfam (PF01783) In PDB	Thermus thermophilus HB8
28	16, 26	50S ribosomal protein L33	polymer	53	6501.7	2	UniProt (P35871) Pfam (PF00471) In PDB	Thermus thermophilus HB8
29	17, 27	50S ribosomal protein L34	polymer	48	5975.3	2	UniProt (P80340) Pfam (PF00468) In PDB	Thermus thermophilus HB8
30	18, 28	50S ribosomal protein L35	polymer	64	7375.0	2	UniProt (Q5SKU1) Pfam (PF01632) In PDB	Thermus thermophilus HB8
31	19, 29	50S ribosomal protein L36	polymer	37	4435.4	2	UniProt (Q5SHR2) Pfam (PF00444) In PDB	Thermus thermophilus HB8	Ribosomal protein B
32	1a, 2a	16S ribosomal RNA	polymer	1521	493863.6	2	GenBank (55771382)	Thermus thermophilus HB8
33	2x, 1x	Ribosome-associated inhibitor A	polymer	97	10964.6	2	UniProt (P0AD49) Pfam (PF02482) In PDB	Escherichia coli K-12	Protein Y,SpotY,pY
34	1b, 2b	30S ribosomal protein S2	polymer	231	26646.9	2	UniProt (P80371) Pfam (PF00318) In PDB	Thermus thermophilus HB8
35	1c, 2c	30S ribosomal protein S3	polymer	206	22862.4	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189) In PDB	Thermus thermophilus HB8
36	1d, 2d	30S ribosomal protein S4	polymer	208	24242.3	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479) In PDB	Thermus thermophilus HB8
37	1e, 2e	30S ribosomal protein S5	polymer	148	16144.8	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719) In PDB	Thermus thermophilus HB8
38	1f, 2f	30S ribosomal protein S6	polymer	100	11917.7	2	UniProt (Q5SLP8) Pfam (PF01250) In PDB	Thermus thermophilus HB8	TS9
39	1g, 2g	30S ribosomal protein S7	polymer	155	17919.8	2	UniProt (P17291) Pfam (PF00177) In PDB	Thermus thermophilus HB8
40	1h, 2h	30S ribosomal protein S8	polymer	137	15737.4	2	UniProt (Q5SHQ2) In PDB	Thermus thermophilus HB8
41	1i, 2i	30S ribosomal protein S9	polymer	127	14279.4	2	UniProt (P80374) Pfam (PF00380) In PDB	Thermus thermophilus HB8
42	1j, 2j	30S ribosomal protein S10	polymer	97	11170.0	2	UniProt (Q5SHN7) Pfam (PF00338) In PDB	Thermus thermophilus HB8
43	1k, 2k	30S ribosomal protein S11	polymer	114	12032.7	2	UniProt (P80376) Pfam (PF00411) In PDB	Thermus thermophilus HB8
44	1l, 2l	30S ribosomal protein S12	polymer	122	13650.2	2	UniProt (Q5SHN3) Pfam (PF00164) In PDB	Thermus thermophilus HB8
45	1m, 2m	30S ribosomal protein S13	polymer	116	13237.4	2	UniProt (P80377) Pfam (PF00416) In PDB	Thermus thermophilus HB8
46	1n, 2n	30S ribosomal protein S14 type Z	polymer	60	7027.5	2	UniProt (Q5SHQ1) In PDB	Thermus thermophilus HB8
47	1o, 2o	30S ribosomal protein S15	polymer	88	10447.2	2	UniProt (Q5SJ76) Pfam (PF00312) In PDB	Thermus thermophilus HB8
48	1p, 2p	30S ribosomal protein S16	polymer	82	9795.4	2	UniProt (Q5SJH3) Pfam (PF00886) In PDB	Thermus thermophilus HB8
49	1q, 2q	30S ribosomal protein S17	polymer	99	11722.9	2	UniProt (Q5SHP7) In PDB	Thermus thermophilus HB8
50	1r, 2r	30S ribosomal protein S18	polymer	68	7897.5	2	UniProt (Q5SLQ0) Pfam (PF01084) In PDB	Thermus thermophilus HB8
51	1s, 2s	30S ribosomal protein S19	polymer	83	9456.0	2	UniProt (Q5SHP2) Pfam (PF00203) In PDB	Thermus thermophilus HB8
52	1t, 2t	30S ribosomal protein S20	polymer	98	10876.1	2	UniProt (P80380) Pfam (PF01649) In PDB	Thermus thermophilus HB8
53	1u, 2u	30S ribosomal protein Thx	polymer	23	2831.3	2	UniProt (Q5SIH3) Pfam (PF17070) In PDB	Thermus thermophilus HB8	S31
54	1y, 2y	Pyrrhocoricin	polymer	16	1796.1	2	UniProt (P37362) In PDB	Pyrrhocoris apterus
55	1A, 1a, 2A, 1o, 2B...	MAGNESIUM ION	non-polymer		24.3	2420	Chemie (MG)
56	24, 14, 25, 15, 26...	ZINC ION	non-polymer		65.4	12	Chemie (ZN)
57	2d, 1d	IRON/SULFUR CLUSTER	non-polymer		351.6	2	Chemie (SF4)
58	2A	ADENOSINE-5'-MONOPHOSPHATE	non-polymer		347.2	1	Chemie (A)
59		water	water		18.0	4546	Chemie (HOH)

Contents of the asymmetric unit

Polymers	Number of chains	108
	Total formula weight	4308405.4
Non-Polymers*	Number of molecules	2435
	Total formula weight	60653.5
All*	Total formula weight	4369058.9

*Water molecules are not included.