2QEX

Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 (0)	23S ribosomal RNA	polymer	2772	897730.6	1		Haloarcula marismortui
2	B (9)	5S ribosomal RNA	polymer	122	39318.4	1	GenBank (6468293)	Haloarcula marismortui
3	C (A)	50S ribosomal protein L2P	polymer	240	25354.7	1	UniProt (P20276) Pfam (PF00181) Pfam (PF03947)	Haloarcula marismortui
4	D (B)	50S ribosomal protein L3P	polymer	338	37396.4	1	UniProt (P20279) Pfam (PF00297)	Haloarcula marismortui
5	E (C)	50S ribosomal protein L4P	polymer	246	26442.1	1	UniProt (P12735) Pfam (PF00573)	Haloarcula marismortui
6	F (D)	50S ribosomal protein L5P	polymer	177	19551.7	1	UniProt (P14124) Pfam (PF00281) Pfam (PF00673)	Haloarcula marismortui
7	G (E)	50S ribosomal protein L6P	polymer	178	19961.7	1	UniProt (P14135) Pfam (PF00347)	Haloarcula marismortui
8	H (F)	50S ribosomal protein L7Ae	polymer	120	12791.9	1	UniProt (P12743) Pfam (PF01248)	Haloarcula marismortui
9	I (G)	Acidic ribosomal protein P0 homolog	polymer	348	37213.8	1	UniProt (P15825) Pfam (PF00466) Pfam (PF17777)	Haloarcula marismortui
10	J (H)	50S ribosomal protein L10e	polymer	174	19402.0	1	UniProt (P60617) Pfam (PF00252)	Haloarcula marismortui
11	K (J)	50S ribosomal protein L13P	polymer	145	16249.2	1	UniProt (P29198) Pfam (PF00572)	Haloarcula marismortui
12	L (K)	50S ribosomal protein L14P	polymer	132	14191.2	1	UniProt (P22450) Pfam (PF00238)	Haloarcula marismortui
13	M (L)	50S ribosomal protein L15P	polymer	165	18005.4	1	UniProt (P12737) Pfam (PF00828)	Haloarcula marismortui
14	N (M)	50S ribosomal protein L15e	polymer	196	22418.3	1	UniProt (P60618) Pfam (PF00827)	Haloarcula marismortui
15	O (N)	50S ribosomal protein L18P	polymer	187	20640.9	1	UniProt (P14123) Pfam (PF17144)	Haloarcula marismortui
16	P (O)	50S ribosomal protein L18e	polymer	116	12438.9	1	UniProt (P12733) Pfam (PF00828)	Haloarcula marismortui
17	Q (P)	50S ribosomal protein L19e	polymer	149	16796.5	1	UniProt (P14119) Pfam (PF01280)	Haloarcula marismortui
18	R (Q)	50S ribosomal protein L21e	polymer	96	10567.8	1	UniProt (P12734) Pfam (PF01157)	Haloarcula marismortui
19	S (R)	50S ribosomal protein L22P	polymer	155	16966.9	1	UniProt (P10970) Pfam (PF00237)	Haloarcula marismortui
20	T (S)	50S ribosomal protein L23P	polymer	85	9612.5	1	UniProt (P12732) Pfam (PF00276)	Haloarcula marismortui
21	U (T)	50S ribosomal protein L24P	polymer	120	13671.0	1	UniProt (P10972) Pfam (PF16906) Pfam (PF00467)	Haloarcula marismortui
22	V (U)	50S ribosomal protein L24e	polymer	67	7364.9	1	UniProt (P14116) Pfam (PF01246)	Haloarcula marismortui
23	W (V)	50S ribosomal protein L29P	polymer	71	7889.9	1	UniProt (P10971) Pfam (PF00831)	Haloarcula marismortui
24	X (W)	50S ribosomal protein L30P	polymer	154	17062.9	1	UniProt (P14121) Pfam (PF00327)	Haloarcula marismortui
25	Y (X)	50S ribosomal protein L31e	polymer	92	10384.6	1	UniProt (P18138) Pfam (PF01198)	Haloarcula marismortui
26	Z (Y)	50S ribosomal protein L32e	polymer	241	26455.7	1	UniProt (P12736) Pfam (PF14520) Pfam (PF01655)	Haloarcula marismortui
27	AA (Z)	50S ribosomal protein L37Ae	polymer	73	8294.2	1	UniProt (P60619) Pfam (PF01780)	Haloarcula marismortui
28	BA (1)	50S ribosomal protein L37e	polymer	57	6330.2	1	UniProt (P32410) Pfam (PF01907)	Haloarcula marismortui
29	CA (2)	50S ribosomal protein L39e	polymer	50	6133.1	1	UniProt (P22452) Pfam (PF00832)	Haloarcula marismortui
30	DA (3)	50S ribosomal protein L44e	polymer	92	10815.2	1	UniProt (P32411) Pfam (PF00935)	Haloarcula marismortui
31	EA (I)	50S ribosomal protein L11P	polymer	162	17097.5	1	UniProt (P14122) Pfam (PF03946) Pfam (PF00298)	Haloarcula marismortui
32	AB, AC, AD, AE, AJ... (0, 3, K, 9, A...)	MAGNESIUM ION	non-polymer		24.3	116	Chemie (MG)
33	JE, KE (0)	POTASSIUM ION	non-polymer		39.1	2	Chemie (K)
34	AF, AG, AH, AI, BF... (0, C, H, J, L...)	SODIUM ION	non-polymer		23.0	86	Chemie (NA)
35	CJ, DI, EI, FH, FI... (3, J, 0, L, M...)	CHLORIDE ION	non-polymer		35.5	22	Chemie (CL)
36	PH (0)	NEGAMYCIN	non-polymer		248.3	1	Chemie (NEG)
37	BJ, MI, WI, YI, ZI (3, O, U, Z, 1)	CADMIUM ION	non-polymer		112.4	5	Chemie (CD)
38	AK, BK, CK, DJ, DK... (W, X, Y, 0, Z...)	water	water		18.0	7788	Chemie (HOH)

Sequence modifications

9: 3001 - 3122 (GenBank: 6468293)

PDB	External Database	Details
G 3073	A 215	conflict
C 3106	U 248	conflict

C: 1 - 246 (UniProt: P12735)

PDB	External Database	Details
Leu 73	Gln 73	conflict

G: 1 - 348 (UniProt: P15825)

PDB	External Database	Details
Asp 248	Ala 248	conflict

H: -2 - 171 (UniProt: P60617)

PDB	External Database	Details
Asp 164	-	insertion
Ser 165	Lys 167	conflict
Ser 166	Val 168	conflict
Pro 167	Glu 169	conflict
Ala 168	Arg 170	conflict
-	Glu 172	deletion
-	Glu 173	deletion
-	Leu 174	deletion
-	Leu 175	deletion
Asn 170	Ile 176	conflict

K: 1 - 132 (UniProt: P22450)

PDB	External Database	Details
Leu 44	His 44	conflict

M: 0 - 195 (UniProt: P60618)

PDB	External Database	Details
Glu 13	Lys 14	conflict
Ala 194	Gly 195	conflict

Z: 10 - 82 (UniProt: P60619)

PDB	External Database	Details
Arg 10	Ser 10	conflict

Contents of the asymmetric unit

Polymers	Number of chains	31
	Total formula weight	1424550.3
Non-Polymers*	Number of molecules	232
	Total formula weight	6465.0
All*	Total formula weight	1431015.3

*Water molecules are not included.