5MEI

Crystal structure of Agelastatin A bound to the 80S 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, UA (1, AR)	25S ribosomal RNA	polymer	3396	1097493.9	2	REF (831416132)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
2	B, VA (3, AS)	5S ribosomal RNA	polymer	121	38951.1	2	GenBank (1039024062)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
3	C, WA (4, AT)	5.8S ribosomal RNA	polymer	158	50682.9	2	GenBank (1102645687)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
4	D, XA (j, CD)	60S ribosomal protein L2-A	polymer	252	27217.3	2	UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L5,RP8,YL6
5	E, YA (k, CE)	60S ribosomal protein L3	polymer	386	43719.6	2	UniProt (P14126) Pfam (PF00297)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
6	F, ZA (l, CF)	60S ribosomal protein L4-A	polymer	361	39027.9	2	UniProt (P10664) Pfam (PF00573) Pfam (PF14374)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L2,RP2,YL2
7	AB, G (m, CG)	60S ribosomal protein L5	polymer	296	33633.6	2	UniProt (P26321) Pfam (PF17144) Pfam (PF14204)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L1,L1a,Ribosomal 5S RNA-binding protein,YL3
8	BB, H (n, CH)	60S ribosomal protein L6-A	polymer	175	19869.4	2	UniProt (Q02326) Pfam (PF01159)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L17,RP18,YL16
9	CB, I (o, CI)	60S ribosomal protein L7-A	polymer	222	25240.4	2	UniProt (P05737) Pfam (PF08079) Pfam (PF00327)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L6,RP11,YL8
10	DB, J (p, CJ)	60S ribosomal protein L8-A	polymer	233	25815.0	2	UniProt (P17076) Pfam (PF01248)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
11	EB, K (q, CK)	60S ribosomal protein L9-A	polymer	191	21605.1	2	UniProt (P05738) Pfam (PF00347)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L8,RP24,YL11
12	FB, L (r, CL)	60S ribosomal protein L10	polymer	220	25279.3	2	UniProt (P41805) Pfam (PF00252)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
13	GB, M (s, CM)	60S ribosomal protein L11-B	polymer	169	19266.1	2	UniProt (Q3E757) Pfam (PF00281) Pfam (PF00673)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L16,RP39,YL22
14	HB, N (t, CN)	60S ribosomal protein L13-A	polymer	193	21885.2	2	UniProt (Q12690) Pfam (PF01294)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
15	IB, O (u, CO)	60S ribosomal protein L14-A	polymer	136	14976.8	2	UniProt (P36105) Pfam (PF00467) Pfam (PF01929)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
16	JB, P (v, CP)	60S ribosomal protein L15-A	polymer	203	24351.2	2	UniProt (P05748) Pfam (PF00827)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L13,RP15R,YL10,YP18
17	KB, Q (w, CQ)	60S ribosomal protein L16-A	polymer	197	22029.0	2	UniProt (P26784) Pfam (PF00572)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L13a,L21,RP22,YL15
18	LB, R (x, CR)	60S ribosomal protein L17-A	polymer	183	20458.3	2	UniProt (P05740) Pfam (PF00237)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L20A,YL17
19	MB, S (y, CS)	60S ribosomal protein L18-A	polymer	185	20478.1	2	UniProt (P0CX49) Pfam (PF17135)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP28
20	NB, T (z, CT)	60S ribosomal protein L19-A	polymer	188	21631.1	2	UniProt (P0CX82) Pfam (PF01280)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L23,RP15L,RP33,YL14
21	OB, U (0, CU)	60S ribosomal protein L20-A	polymer	172	20478.9	2	UniProt (P0CX23) Pfam (PF01775)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L18a
22	PB, V (2, CV)	60S ribosomal protein L21-A	polymer	159	18148.1	2	UniProt (Q02753) Pfam (PF01157)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
23	QB, W (5, CW)	60S ribosomal protein L22-A	polymer	100	11263.9	2	UniProt (P05749) Pfam (PF01776)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L1c,RP4,YL31
24	RB, X (l2, CX)	60S ribosomal protein L23-A	polymer	136	14362.8	2	UniProt (P0CX41) Pfam (PF00238)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L17a,YL32
25	OC, Y (6, A)	18S ribosomal RNA	polymer	1800	579761.9	2	GenBank (874346701)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
26	SB, Z (7, CY)	60S ribosomal protein L24-A	polymer	98	11369.4	2	UniProt (P04449) Pfam (PF01246)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L30,RP29,YL21
27	AA, TB (8, CZ)	60S ribosomal protein L25	polymer	121	13771.2	2	UniProt (P04456) Pfam (PF03939) Pfam (PF00276)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP16L,YL25,YP42'
28	BA, UB (9, DA)	60S ribosomal protein L26-A	polymer	126	14134.6	2	UniProt (P05743) Pfam (PF16906) Pfam (PF00467)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L33,YL33
29	CA, VB (AA, DB)	60S ribosomal protein L27-A	polymer	135	15437.2	2	UniProt (P0C2H6) Pfam (PF01777)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
30	DA, WB (AB, DC)	60S ribosomal protein L28	polymer	148	16630.5	2	UniProt (P02406) Pfam (PF00828)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L27a,L29,RP44,RP62,YL24
31	EA, XB (AC, DD)	60S ribosomal protein L29	polymer	58	6560.7	2	UniProt (P05747) Pfam (PF01779)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	YL43
32	FA, YB (AD, DE)	60S ribosomal protein L30	polymer	97	10558.3	2	UniProt (P14120) Pfam (PF01248)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L32,RP73,YL38
33	GA, ZB (AE, DF)	60S ribosomal protein L31-A	polymer	109	12649.8	2	UniProt (P0C2H8) Pfam (PF01198)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L34,YL28
34	AC, HA (AF, DG)	60S ribosomal protein L32	polymer	127	14478.1	2	UniProt (P38061) Pfam (PF01655)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
35	BC, IA (AG, DH)	60S ribosomal protein L33-A	polymer	106	12045.9	2	UniProt (P05744) Pfam (PF01247)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L37,RP47,YL37
36	CC, JA (AH, DI)	60S ribosomal protein L34-A	polymer	112	12608.8	2	UniProt (P87262) Pfam (PF01199)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
37	DC, KA (AI, DJ)	60S ribosomal protein L35-A	polymer	119	13811.4	2	UniProt (P0CX84) Pfam (PF00831)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
38	EC, LA (AJ, DK)	60S ribosomal protein L36-A	polymer	99	11020.1	2	UniProt (P05745) Pfam (PF01158)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L39,YL39
39	FC, MA (AK, DL)	60S ribosomal protein L37-A	polymer	87	9746.2	2	UniProt (P49166) Pfam (PF01907)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L43,YL35,YP55
40	GC, NA (AL, DM)	60S ribosomal protein L38	polymer	77	8714.4	2	UniProt (P49167) Pfam (PF01781)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
41	HC, OA (AM, DN)	60S ribosomal protein L39	polymer	50	6227.4	2	UniProt (P04650) Pfam (PF00832)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L46,YL40
42	IC, PA (AN, DO)	Ubiquitin-60S ribosomal protein L40	polymer	52	6032.3	2	UniProt (P0CH08) Pfam (PF01020)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
43	JC, QA (AO, DP)	60S ribosomal protein L41-B	polymer	25	3354.2	2	UniProt (P0CX87) Pfam (PF05162) UniProt (by SIFTS) (P0CX86)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L47,YL41
44	KC, RA (AP, DQ)	60S ribosomal protein L42-A	polymer	105	12115.5	2	UniProt (P0CX27) Pfam (PF00935)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L41,YL27,YP44
45	LC, SA (AQ, DR)	60S ribosomal protein L43-A	polymer	91	9981.8	2	UniProt (P0CX25) Pfam (PF01780)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L37a,YL35
46	TA (i)	Suppressor protein STM1	polymer	168	18225.0	1	UniProt (P39015) Pfam (PF09598)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	3BP1,GU4 nucleic-binding protein 2,G4p2 protein,POP2 multicopy suppressor protein 4,Ribosomal subunits association factor,AF,TOM1 suppressor protein 1,Triplex-binding protein 1
47	MC (p0)	60S acidic ribosomal protein P0	polymer	220	24101.7	1	UniProt (P05317) Pfam (PF00466) Pfam (PF17777)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	A0,L10E
48	NC (sM)	Suppressor protein STM1,Suppressor protein STM1,Suppressor protein Stm1 - Mol B	polymer	104	10296.9	1	UniProt (P39015) Pfam (PF09598)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	3BP1,GU4 nucleic-binding protein 2,G4p2 protein,POP2 multicopy suppressor protein 4,Ribosomal subunits association factor,AF,TOM1 suppressor protein 1,Triplex-binding protein 1,3BP1,GU4 nucleic-binding protein 2,G4p2 protein,POP2 multicopy suppressor protein 4,Ribosomal subunits association factor,AF,TOM1 suppressor protein 1,Triplex-binding protein 1
49	PC, WD (B, s0)	40S ribosomal protein S0-A	polymer	206	22811.1	2	UniProt (P32905) Pfam (PF00318)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Nucleic acid-binding protein NAB1A
50	QC, XD (C, s1)	40S ribosomal protein S1-A	polymer	216	24498.4	2	UniProt (P33442) Pfam (PF01015)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP10A
51	RC, YD (D, s2)	40S ribosomal protein S2	polymer	217	23213.0	2	UniProt (P25443) Pfam (PF00333) Pfam (PF03719)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Omnipotent suppressor protein SUP44,RP12,S4,YS5
52	SC, ZD (E, s3)	40S ribosomal protein S3	polymer	223	24702.8	2	UniProt (P05750) Pfam (PF07650) Pfam (PF00189)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP13,YS3
53	AE, TC (F, s4)	40S ribosomal protein S4-A	polymer	260	29338.1	2	UniProt (P0CX35) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP5,S7,YS6
54	BE, UC (G, s5)	40S ribosomal protein S5	polymer	206	22908.3	2	UniProt (P26783) Pfam (PF00177)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP14,S2,YS8
55	CE, VC (H, s6)	40S ribosomal protein S6-A	polymer	226	25895.1	2	UniProt (P0CX37) Pfam (PF01092)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP9,S10,YS4
56	DE, WC (I, s7)	40S ribosomal protein S7-A	polymer	186	21158.6	2	UniProt (P26786) Pfam (PF01251)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP30,RP40
57	EE, XC (J, s8)	40S ribosomal protein S8-A	polymer	199	22406.6	2	UniProt (P0CX39) Pfam (PF01201)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP19,S14,YS9
58	FE, YC (K, s9)	40S ribosomal protein S9-A	polymer	185	21210.7	2	UniProt (O13516) Pfam (PF00163) Pfam (PF01479)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP21,S13,YP28,YS11
59	GE, ZC (L, c0)	40S ribosomal protein S10-A	polymer	105	12757.4	2	UniProt (Q08745) Pfam (PF03501)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
60	AD, HE (M, c1)	40S ribosomal protein S11-A	polymer	155	17654.7	2	UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP41,S18,YS12
61	BD, IE (N, c2)	40S ribosomal protein S12	polymer	124	13327.3	2	UniProt (P48589) Pfam (PF01248)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
62	CD, JE (O, c3)	40S ribosomal protein S13	polymer	150	16928.7	2	UniProt (P05756) Pfam (PF08069) Pfam (PF00312)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	S27a,YS15
63	DD, KE (P, c4)	40S ribosomal protein S14-B	polymer	128	13560.5	2	UniProt (P39516) Pfam (PF00411)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP59B
64	ED, LE (Q, c5)	40S ribosomal protein S15	polymer	141	15900.7	2	UniProt (Q01855) Pfam (PF00203)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RIG protein,RP52,S21,YS21
65	FD, ME (R, c6)	40S ribosomal protein S16-A	polymer	142	15746.3	2	UniProt (P0CX51) Pfam (PF00380)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP61R
66	GD (S)	40S ribosomal protein S17-B	polymer	125	14268.5	1	UniProt (P14127) Pfam (PF00833)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP51B
67	HD, OE (T, c8)	40S ribosomal protein S18-A	polymer	145	16940.4	2	UniProt (P0CX55) Pfam (PF00416)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
68	ID, PE (U, c9)	40S ribosomal protein S19-A	polymer	143	15810.9	2	UniProt (P07280) Pfam (PF01090)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP55A,S16a,YP45,YS16A
69	JD, QE (V, d0)	40S ribosomal protein S20	polymer	110	12575.5	2	UniProt (P38701) Pfam (PF00338)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
70	KD, RE (W, d1)	40S ribosomal protein S21-A	polymer	87	9758.8	2	UniProt (P0C0V8) Pfam (PF01249)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	S26,YS25
71	LD, SE (X, d2)	40S ribosomal protein S22-A	polymer	129	14518.9	2	UniProt (P0C0W1) Pfam (PF00410)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP50,S24,YP58,YS22
72	MD, TE (Y, d3)	40S ribosomal protein S23-A	polymer	144	15942.7	2	UniProt (P0CX29) Pfam (PF00164)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP37,S28,YS14
73	ND, UE (Z, d4)	40S ribosomal protein S24-A	polymer	134	15231.6	2	UniProt (P0CX31) Pfam (PF01282)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP50
74	OD, VE (a, d5)	40S ribosomal protein S25-A	polymer	70	8001.4	2	UniProt (Q3E792) Pfam (PF03297)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP45,S31,YS23
75	PD, WE (b, d6)	40S ribosomal protein S26-B	polymer	97	11023.0	2	UniProt (P39939) Pfam (PF01283)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
76	QD, XE (c, d7)	40S ribosomal protein S27-A	polymer	81	8762.2	2	UniProt (P35997) Pfam (PF01667)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP61,YS20
77	RD, YE (d, d8)	40S ribosomal protein S28-A	polymer	63	7116.3	2	UniProt (Q3E7X9) Pfam (PF01200)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	S33,YS27
78	SD, ZE (e, d9)	40S ribosomal protein S29-A	polymer	53	6335.3	2	UniProt (P41057) Pfam (PF00253)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	S36,YS29
79	AF, TD (f, e0)	40S ribosomal protein S30-A	polymer	62	7006.3	2	UniProt (P0CX33) Pfam (PF04758)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
80	UD (g)	Ubiquitin-40S ribosomal protein S31	polymer	71	8101.7	1	UniProt (P05759) Pfam (PF01599)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
81	CF, VD (h, sR)	Guanine nucleotide-binding protein subunit beta-like protein	polymer	318	34710.0	2	UniProt (P38011) Pfam (PF00400)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
82	NE (c7)	40S ribosomal protein S17-A	polymer	121	13897.2	1	UniProt (P02407) Pfam (PF00833)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP51A
83	BF (e1)	Ubiquitin-40S ribosomal protein S31	polymer	51	5704.6	1	UniProt (P05759) Pfam (PF01599)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
84	AAB, ABB, ACB, ADB, AEB... (AK, AR, 1, AS, AT...)	osmium (III) hexammine	non-polymer		286.4	1070	Chemie (OHX)
85	AAA, AAC, ABA, ABC, ACA... (1, AR, AT, CO, DD...)	MAGNESIUM ION	non-polymer		24.3	1406	Chemie (MG)
86	MKA, PGC (1, AR)	Agelastatin A	non-polymer		341.2	2	Chemie (7MB)
87	AWC, CWC, DAB, DWC, EAB... (c, e, AN, g, AP...)	ZINC ION	non-polymer		65.4	16	Chemie (ZN)

Sequence modifications

sM: 23 - 85 (UniProt: P39015)
sM: 119 - 174 (PDB: 5MEI)

Contents of the asymmetric unit

Polymers	Number of chains	159
	Total formula weight	6107848.1
Non-Polymers*	Number of molecules	2494
	Total formula weight	342312.2
All*	Total formula weight	6450160.3

*Water molecules are not included.