1M90

Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	23S RRNA	polymer	2922	946034.4	1	GenBank (3377779)	Haloarcula marismortui
2	B (B)	5S RRNA	polymer	122	39318.4	1	GenBank (3377779)	Haloarcula marismortui
3	C (5)	CCA	polymer	3	894.6	1
4	D (C)	RIBOSOMAL PROTEIN L2	polymer	239	25237.5	1	UniProt (P20276) Pfam (PF00181) Pfam (PF03947)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L2P, HMAL2, HL4
5	E (D)	RIBOSOMAL PROTEIN L3	polymer	337	37265.2	1	UniProt (P20279) Pfam (PF00297)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L3P, HMAL3, HL1
6	F (E)	RIBOSOMAL PROTEIN L4	polymer	246	26442.1	1	UniProt (P12735) Pfam (PF00573)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L4E, HMAL4, HL6
7	G (F)	RIBOSOMAL PROTEIN L5	polymer	176	19420.5	1	UniProt (P14124) Pfam (PF00673) Pfam (PF00281)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L5P, HMAL5, HL13
8	H (G)	RIBOSOMAL PROTEIN L6	polymer	177	19830.5	1	UniProt (P14135) Pfam (PF00347)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L6P, HMAL6, HL10
9	I (H)	RIBOSOMAL PROTEIN L7AE	polymer	119	12600.8	1	UniProt (P12743) Pfam (PF01248)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN HS6
10	J (I)	RIBOSOMAL PROTEIN L10	polymer	348	37213.8	1	UniProt (P15825) Pfam (PF00466) Pfam (PF17777)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN P0, HMAL10, L10E
11	K (J)	RIBOSOMAL PROTEIN L10E	polymer	167	18022.5	1	Pfam (PF00252) UniProt (by SIFTS) (P60617)	Haloarcula marismortui
12	L (K)	RIBOSOMAL PROTEIN L13	polymer	145	16249.2	1	UniProt (P29198) Pfam (PF00572)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L13P, HMAL13
13	M (L)	RIBOSOMAL PROTEIN L14	polymer	132	14216.2	1	UniProt (P22450) Pfam (PF00238)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L14P, HMAL14, HL27
14	N (M)	RIBOSOMAL PROTEIN L15	polymer	164	17874.2	1	UniProt (P12737) Pfam (PF00828)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L15P, HMAL15, HL9
15	O (N)	RIBOSOMAL PROTEIN L15E	polymer	194	22856.6	1	Pfam (PF00827) UniProt (by SIFTS) (P60618)	Haloarcula marismortui
16	P (O)	RIBOSOMAL PROTEIN L18	polymer	186	20509.7	1	UniProt (P14123) Pfam (PF17144)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L18P, HMAL18, HL12
17	Q (P)	RIBOSOMAL PROTEIN L18E	polymer	115	12307.7	1	UniProt (P12733) Pfam (PF00828)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L18E, HL29, L19
18	R (Q)	RIBOSOMAL PROTEIN L19E	polymer	148	16631.3	1	UniProt (P14119) Pfam (PF01280)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L19E, HMAL19, HL24
19	S (R)	RIBOSOMAL PROTEIN L21E	polymer	95	10436.6	1	UniProt (P12734) Pfam (PF01157)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L21E, HL31
20	T (S)	RIBOSOMAL PROTEIN L22	polymer	154	16835.7	1	UniProt (P10970) Pfam (PF00237)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L22P, HMAL22, HL23
21	U (T)	RIBOSOMAL PROTEIN L23	polymer	84	9481.3	1	UniProt (P12732) Pfam (PF00276)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L23P, HMAL23, HL25, L21
22	V (U)	RIBOSOMAL PROTEIN L24	polymer	119	13539.8	1	UniProt (P10972) Pfam (PF16906) Pfam (PF00467)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L24P, HMAL24, HL16, HL15
23	W (V)	RIBOSOMAL PROTEIN L24E	polymer	66	7233.7	1	UniProt (P14116) Pfam (PF01246)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L24E, HL21/HL22
24	X (W)	RIBOSOMAL PROTEIN L29	polymer	70	7758.7	1	UniProt (P10971) Pfam (PF00831)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L29P, HMAL29, HL33
25	Y (X)	RIBOSOMAL PROTEIN L30	polymer	154	17062.9	1	UniProt (P14121) Pfam (PF00327)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L30P, HMAL30, HL20, HL16
26	Z (Y)	RIBOSOMAL PROTEIN L31E	polymer	91	10253.4	1	UniProt (P18138) Pfam (PF01198)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L31E, L34, HL30
27	AA (Z)	RIBOSOMAL PROTEIN L32E	polymer	240	26324.5	1	UniProt (P12736) Pfam (PF14520) Pfam (PF01655)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L32E, HL5
28	BA (1)	RIBOSOMAL PROTEIN L37Ae	polymer	73	8097.8	1	Pfam (PF01780) UniProt (by SIFTS) (P60619)	Haloarcula marismortui
29	CA (2)	RIBOSOMAL PROTEIN L37E	polymer	56	6199.0	1	UniProt (P32410) Pfam (PF01907)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L37E, L35E
30	DA (3)	RIBOSOMAL PROTEIN L39E	polymer	48	5844.7	1	UniProt (P22452) Pfam (PF00832)	Haloarcula marismortui	50S RIBOSOMAL PROTEINS L39E, HL39E, HL46E
31	EA (4)	RIBOSOMAL PROTEIN L44E	polymer	92	10815.2	1	UniProt (P32411) Pfam (PF00935)	Haloarcula marismortui	50S RIBOSOMAL PROTEIN L44E, LA, HLA
32	AB, AC, AD, AE, AI... (A, C, Z, 1, 4...)	MAGNESIUM ION	non-polymer		24.3	119	Chemie (MG)
33	AF, AG, AH, BF, BG... (A, C, E, J, K...)	SODIUM ION	non-polymer		23.0	86	Chemie (NA)
34	HH, IH (A)	POTASSIUM ION	non-polymer		39.1	2	Chemie (K)
35	BJ, CI, DI, HI, HJ... (Z, C, D, K, 4...)	CHLORIDE ION	non-polymer		35.5	22	Chemie (CL)
36	WH (5)	SPARSOMYCIN	non-polymer		361.4	1	Chemie (SPS)
37	YH (5)	PHENYLALANINAL	non-polymer		149.2	1	Chemie (PHA)
38	ZH (5)	6-AMINOHEXANOIC ACID	non-polymer		131.2	1	Chemie (ACA)
39	DJ, EJ, GJ, QI, ZI (1, 2, 4, P, V)	CADMIUM ION	non-polymer		112.4	5	Chemie (CD)
40	AK, BK, CK, DK, EK... (R, S, T, U, V...)	water	water		18.0	7858	Chemie (HOH)

Sequence modifications

A: 2 - 2923 (GenBank: 3377779)

PDB	External Database	Details
C 560	U 3155	conflict

D: 1 - 337 (UniProt: P20279)

PDB	External Database	Details
-	Pro 310	deletion
Arg 310	Phe 311	conflict

Q: 1 - 148 (UniProt: P14119)

PDB	External Database	Details
Lys 71	Tyr 71	conflict

3: 1 - 48 (UniProt: P22452)

PDB	External Database	Details
-	Arg 31	deletion

Contents of the asymmetric unit

Polymers	Number of chains	31
	Total formula weight	1452808.8
Non-Polymers*	Number of molecules	237
	Total formula weight	6931.5
All*	Total formula weight	1459740.2

*Water molecules are not included.