Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7MDZ

80S rabbit ribosome stalled with benzamide-CHX

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 (A)	Ribosomal protein L8	polymer	257	28088.9	1	UniProt (G1TT27) Pfam (PF00181) Pfam (PF03947)	Oryctolagus cuniculus (Rabbit)
2	B (B)	uL3	polymer	403	46108.0	1	UniProt (G1TL06) Pfam (PF00297)	Oryctolagus cuniculus (Rabbit)
3	C (C)	60S ribosomal protein L4	polymer	425	47727.6	1	UniProt (G1SVW5) Pfam (PF00573) Pfam (PF14374)	Oryctolagus cuniculus (Rabbit)
4	D (D)	Ribosomal_L18_c domain-containing protein	polymer	297	34481.8	1	UniProt (G1SYJ6) UniProt (by SIFTS) (P19949)	Oryctolagus cuniculus (Rabbit)
5	E (E)	60S ribosomal protein L6	polymer	291	33028.3	1	UniProt (G1SKF7) Pfam (PF03868) Pfam (PF01159)	Oryctolagus cuniculus (Rabbit)
6	F (F)	60S ribosomal protein L7	polymer	247	29201.8	1	UniProt (G1TUB1) Pfam (PF08079) Pfam (PF00327) UniProt (by SIFTS) (G1SV32)	Oryctolagus cuniculus (Rabbit)
7	G (G)	60S ribosomal protein L7a	polymer	319	36221.5	1	UniProt (G1STW0) Pfam (PF01248)	Oryctolagus cuniculus (Rabbit)
8	H (H)	60S ribosomal protein L9	polymer	192	21871.4	1	UniProt (G1SWI6) Pfam (PF00347)	Oryctolagus cuniculus (Rabbit)
9	I (I)	60S ribosomal protein L10	polymer	214	24643.1	1	UniProt (B7NZQ2) Pfam (PF00252)	Oryctolagus cuniculus (Rabbit)
10	J (J)	60S ribosomal protein L11	polymer	178	20288.5	1	UniProt (G1TUB8) Pfam (PF00281) Pfam (PF00673)	Oryctolagus cuniculus (Rabbit)
11	K (L)	60S ribosomal protein L13	polymer	211	24331.7	1	UniProt (G1TPV0)	Oryctolagus cuniculus (Rabbit)
12	L (M)	60S ribosomal protein L14	polymer	218	23870.5	1	UniProt (G1SZ12) Pfam (PF01929)	Oryctolagus cuniculus (Rabbit)
13	M (N)	Ribosomal protein L15	polymer	204	24207.3	1	UniProt (G1T0C1) Pfam (PF00827)	Oryctolagus cuniculus (Rabbit)
14	N (O)	uL13	polymer	203	23533.3	1		Oryctolagus cuniculus
15	O (P)	uL22	polymer	184	21444.2	1	UniProt (G1TVT6) Pfam (PF00237) UniProt (by SIFTS) (G1SCJ6)	Oryctolagus cuniculus (Rabbit)
16	P (Q)	Ribosomal protein L18	polymer	188	21699.7	1	UniProt (G1TFE0) Pfam (PF17135)	Oryctolagus cuniculus (Rabbit)
17	Q (R)	Ribosomal protein L19	polymer	196	23535.3	1	UniProt (G1TJR3) Pfam (PF01280) UniProt (by SIFTS) (G1TYL6)	Oryctolagus cuniculus (Rabbit)
18	R (S)	60S ribosomal protein L18a	polymer	176	20827.6	1	UniProt (G1TTY7) Pfam (PF01775)	Oryctolagus cuniculus (Rabbit)
19	S (T)	eL21	polymer	160	18610.0	1	UniProt (G1SHQ2) Pfam (PF01157)	Oryctolagus cuniculus (Rabbit)
20	T (U)	eL22	polymer	128	14813.0	1	UniProt (G1TSG1) Pfam (PF01776)	Oryctolagus cuniculus (Rabbit)
21	U (V)	Ribosomal protein L23	polymer	140	14892.5	1	UniProt (G1T6D1) Pfam (PF00238)	Oryctolagus cuniculus (Rabbit)
22	V (W)	60S ribosomal protein L24	polymer	157	17825.1	1	UniProt (G1SE28) Pfam (PF01246)	Oryctolagus cuniculus (Rabbit)
23	W (X)	eL23	polymer	156	17768.2	1	UniProt (G1SE76) Pfam (PF03939) Pfam (PF00276)	Oryctolagus cuniculus (Rabbit)
24	X (Y)	uL24	polymer	145	17303.4	1	UniProt (G1SQH0) Pfam (PF16906) Pfam (PF00467)	Oryctolagus cuniculus (Rabbit)
25	Y (Z)	60S ribosomal protein L27	polymer	136	15835.8	1	UniProt (G1TXF6) Pfam (PF00467) Pfam (PF01777)	Oryctolagus cuniculus (Rabbit)
26	Z (a)	60S ribosomal protein L27a	polymer	148	16620.6	1	UniProt (G1SNY0) Pfam (PF00828)	Oryctolagus cuniculus (Rabbit)
27	AA (b)	60S ribosomal protein L29	polymer	245	26708.7	1	UniProt (G1SGR6) Pfam (PF01779)	Oryctolagus cuniculus (Rabbit)
28	BA (c)	eL30	polymer	115	12807.1	1	UniProt (G1TDL2) Pfam (PF01248)	Oryctolagus cuniculus (Rabbit)
29	CA (d)	eL31	polymer	125	14494.9	1	UniProt (G1SHG0) Pfam (PF01198)	Oryctolagus cuniculus (Rabbit)
30	DA (e)	eL32	polymer	135	15898.9	1	UniProt (G1U437) Pfam (PF01655) UniProt (by SIFTS) (G1TUN8)	Oryctolagus cuniculus (Rabbit)
31	EA (f)	eL33	polymer	110	12580.8	1	UniProt (G1SF08) Pfam (PF01247)	Oryctolagus cuniculus (Rabbit)
32	FA (g)	60S ribosomal protein L34	polymer	116	13196.9	1	UniProt (G1U945) Pfam (PF01199) UniProt (by SIFTS) (G1TXG5)	Oryctolagus cuniculus (Rabbit)
33	GA (h)	eL35	polymer	123	14566.6	1	UniProt (G1SIT5) Pfam (PF00831)	Oryctolagus cuniculus (Rabbit)
34	HA (i)	60S ribosomal protein L36	polymer	105	12263.8	1	UniProt (G1TTQ5) Pfam (PF01158)	Oryctolagus cuniculus (Rabbit)
35	IA (j)	Ribosomal protein L37	polymer	97	11111.0	1	UniProt (U3KPD5) Pfam (PF01907)	Oryctolagus cuniculus (Rabbit)
36	JA (k)	60S ribosomal protein L38	polymer	70	8238.9	1	UniProt (G1U001) Pfam (PF01781)	Oryctolagus cuniculus (Rabbit)
37	KA (l)	eL39	polymer	51	6455.8	1	UniProt (G1TTN1) Pfam (PF00832) UniProt (by SIFTS) (G1SYU7)	Oryctolagus cuniculus (Rabbit)
38	LA (m)	eL40	polymer	102	11699.8	1		Oryctolagus cuniculus
39	MA (n)	60s ribosomal protein l41	polymer	25	3473.5	1	UniProt (A0A087WNH4) Pfam (PF05162)	Oryctolagus cuniculus (Rabbit)
40	NA (o)	eL42	polymer	106	12477.0	1	UniProt (G1U344) Pfam (PF00935) UniProt (by SIFTS) (G1T040)	Oryctolagus cuniculus (Rabbit)
41	OA (p)	eL43	polymer	92	10299.4	1	UniProt (G1SY53) Pfam (PF01780)	Oryctolagus cuniculus (Rabbit)
42	PA (r)	eL28	polymer	137	15783.6	1	UniProt (G1U7L1) Pfam (PF01778)	Oryctolagus cuniculus (Rabbit)
43	QA (AA)	40S ribosomal protein SA	polymer	295	32958.0	1	UniProt (G1TLT8) Pfam (PF00318) Pfam (PF16122)	Oryctolagus cuniculus (Rabbit)	37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40
44	RA (BB)	eS1	polymer	264	30002.1	1	UniProt (G1SS70) Pfam (PF01015)	Oryctolagus cuniculus (Rabbit)	40S ribosomal protein S3a
45	SA (CC)	uS5	polymer	293	31327.4	1		Oryctolagus cuniculus
46	TA (DD)	Ribosomal protein S3	polymer	243	26715.3	1	UniProt (G1TNM3) Pfam (PF07650) Pfam (PF00189)	Oryctolagus cuniculus (Rabbit)
47	UA (EE)	40S ribosomal protein S4	polymer	263	29654.9	1	UniProt (G1TK17) Pfam (PF08071) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121)	Oryctolagus cuniculus (Rabbit)
48	VA (FF)	uS7	polymer	204	22913.5	1	UniProt (G1TFM5) Pfam (PF00177)	Oryctolagus cuniculus (Rabbit)	40S ribosomal protein S5
49	WA (GG)	eS6	polymer	249	28751.9	1	UniProt (G1TM55) Pfam (PF01092)	Oryctolagus cuniculus (Rabbit)	40S ribosomal protein S6
50	XA (HH)	eS7	polymer	194	22168.9	1	UniProt (G1SVB0)	Oryctolagus cuniculus (Rabbit)	40S ribosomal protein S7
51	YA (II)	eS8	polymer	208	24263.4	1	UniProt (G1TJW1) Pfam (PF01201)	Oryctolagus cuniculus (Rabbit)	40S ribosomal protein S8
52	ZA (JJ)	uS4	polymer	194	22641.6	1	UniProt (B7NZS8) Pfam (PF00163) Pfam (PF01479)	Oryctolagus cuniculus (Rabbit)	Ribosomal protein S9
53	AB (KK)	S10_plectin domain-containing protein	polymer	165	18933.8	1	UniProt (G1TPV3) Pfam (PF03501) UniProt (by SIFTS) (G1T168)	Oryctolagus cuniculus (Rabbit)
54	BB (LL)	uS17	polymer	158	18468.8	1	UniProt (G1TRM4) Pfam (PF16205) Pfam (PF00366)	Oryctolagus cuniculus (Rabbit)	40S ribosomal protein S11
55	CB (MM)	eS12	polymer	132	14539.0	1	UniProt (G1SFR8) Pfam (PF01248)	Oryctolagus cuniculus (Rabbit)	40S ribosomal protein S12
56	DB (NN)	uS15	polymer	151	17259.4	1	UniProt (G1SP51) Pfam (PF08069) Pfam (PF00312)	Oryctolagus cuniculus (Rabbit)	Ribosomal protein S13
57	EB (OO)	uS11	polymer	168	18134.0	1	UniProt (G1U472) Pfam (PF00411) UniProt (by SIFTS) (G1T1F0)	Oryctolagus cuniculus (Rabbit)
58	FB (PP)	uS19	polymer	145	17049.2	1	UniProt (G1U0Q2) Pfam (PF00203)	Oryctolagus cuniculus (Rabbit)
59	GB (QQ)	uS9	polymer	146	16477.4	1	UniProt (G1SGX4) Pfam (PF00380)	Oryctolagus cuniculus (Rabbit)
60	HB (RR)	eS17	polymer	135	15552.1	1	UniProt (G1TU13) Pfam (PF00833)	Oryctolagus cuniculus (Rabbit)
61	IB (SS)	uS13	polymer	152	17759.8	1	UniProt (G1TPG3) Pfam (PF00416)	Oryctolagus cuniculus (Rabbit)
62	JB (TT)	eS19	polymer	145	16106.6	1	UniProt (G1TN62) Pfam (PF01090)	Oryctolagus cuniculus (Rabbit)
63	KB (UU)	uS10	polymer	119	13398.8	1	UniProt (G1SIZ2) Pfam (PF00338)	Oryctolagus cuniculus (Rabbit)
64	LB (VV)	40S ribosomal protein S21	polymer	83	9124.4	1	UniProt (G1TM82) Pfam (PF01249)	Oryctolagus cuniculus (Rabbit)
65	MB (WW)	uS8	polymer	130	14865.6	1	UniProt (G1TG89) Pfam (PF00410)	Oryctolagus cuniculus (Rabbit)	Ribosomal protein S15a
66	NB (XX)	uS12	polymer	143	15844.7	1	UniProt (G1SZ47) Pfam (PF00164)	Oryctolagus cuniculus (Rabbit)
67	OB (YY)	40S ribosomal protein S24	polymer	130	15107.9	1	UniProt (G1T3D8) Pfam (PF01282) UniProt (by SIFTS) (A0A5F9D2E6)	Oryctolagus cuniculus (Rabbit)
68	PB (ZZ)	eS25	polymer	125	13776.2	1	UniProt (G1TDB3) Pfam (PF03297)	Oryctolagus cuniculus (Rabbit)
69	QB (aa)	40S ribosomal protein S26	polymer	115	13047.5	1	UniProt (G1TFE8) Pfam (PF01283)	Oryctolagus cuniculus (Rabbit)
70	RB (bb)	eS27	polymer	84	9480.2	1	UniProt (G1TZ76) Pfam (PF01667)	Oryctolagus cuniculus (Rabbit)	40S ribosomal protein S27
71	SB (cc)	eS28	polymer	69	7855.1	1	UniProt (G1TIB4) Pfam (PF01200)	Oryctolagus cuniculus (Rabbit)	Ribosomal protein S28
72	TB (dd)	eS29	polymer	56	6690.8	1	UniProt (G1U7M4) Pfam (PF00253)	Oryctolagus cuniculus (Rabbit)
73	UB (ee)	eS30	polymer	133	14498.9	1	UniProt (G1T8A2) Pfam (PF00240) Pfam (PF04758)	Oryctolagus cuniculus (Rabbit)	40S ribosomal protein S30
74	VB (ff)	eS31	polymer	156	18004.0	1	UniProt (G1SK22) Pfam (PF00240) Pfam (PF01599)	Oryctolagus cuniculus (Rabbit)	Ribosomal protein S27a
75	WB (gg)	RACK1	polymer	317	35115.7	1	UniProt (G1SJB4) Pfam (PF00400)	Oryctolagus cuniculus (Rabbit)
76	XB (5)	28S rRNA	polymer	3603	1167622.6	1		Oryctolagus cuniculus
77	YB (7)	5S rRNA	polymer	120	38691.9	1	GenBank (X06789.1)	Oryctolagus cuniculus
78	ZB (8)	5.8S rRNA	polymer	156	50143.6	1		Oryctolagus cuniculus
79	AC (2)	P-site tRNA	polymer	76	24485.5	1		Oryctolagus cuniculus
80	BC (9)	18S rRNA	polymer	1869	602777.9	1		Oryctolagus cuniculus
81	CC (6)	mRNA	polymer	10	3139.9	1		synthetic construct
82	AD, AE, AF, AG, AH... (5, 7, 9, A, B...)	MAGNESIUM ION	non-polymer		24.3	277	Chemie (MG)
83	HC, JC, KC, LC, MC... (g, j, m, o, p...)	ZINC ION	non-polymer		65.4	8	Chemie (ZN)
84	WJ (5)	N-[(1R,3S,4R,5S)-3-{(1R)-2-[(2R,4r,6S)-2,6-dihydroxypiperidin-4-yl]-1-hydroxyethyl}-4-hydroxy-1,5-dimethylcyclohexyl]benzamide	non-polymer		400.5	1	Chemie (Z2V)

Sequence modifications

B: 2 - 403 (UniProt: G1TL06)

PDB	External Database	Details
Met 1	-	initiating methionine

C: 1 - 425 (UniProt: G1SVW5)

PDB	External Database	Details
Lys 378	-	insertion
Val 379	-	insertion
Lys 380	-	insertion
Lys 381	-	insertion
Pro 382	-	insertion
Arg 383	-	insertion
Ala 384	-	insertion
Val 385	-	insertion
Gly 386	-	insertion
Ile 387	-	insertion
Lys 388	-	insertion
Gln 389	-	insertion

F: 1 - 247 (UniProt: G1TUB1)

PDB	External Database	Details
Arg 61	Gly 61	conflict
Arg 93	Gly 93	conflict
Met 131	Val 131	conflict
Ile 153	Val 153	conflict

G: 1 - 319 (UniProt: G1STW0)

PDB	External Database	Details
Gly 244	Cys 244	conflict

L: 1 - 211 (UniProt: G1TPV0)

PDB	External Database	Details
Ile 46	-	insertion
Ala 47	-	insertion
Pro 48	-	insertion
Arg 49	-	insertion
Pro 50	-	insertion
Ala 51	-	insertion
Ala 52	-	insertion
Gly 53	-	insertion
Pro 54	-	insertion

Q: 1 - 188 (UniProt: G1TFE0)

PDB	External Database	Details
Asp 4	Asn 4	conflict
Arg 14	Trp 14	conflict
Met 53	Leu 53	conflict
Arg 58	Trp 58	conflict
Arg 75	Gln 75	conflict
Ala 80	Pro 80	conflict
Val 86	Ile 86	conflict
Arg 104	His 104	conflict
Arg 110	Cys 110	conflict
Val 137	Gly 137	conflict
Gly 157	Arg 157	conflict
Arg 181	Trp 181	conflict

R: 1 - 196 (UniProt: G1TJR3)

PDB	External Database	Details
Arg 38	Cys 38	conflict
Arg 64	Gln 64	conflict
Thr 94	Lys 94	conflict

S: 1 - 175 (UniProt: G1TTY7)

PDB	External Database	Details
Met 1	Thr 1	conflict
Pro 18	-	insertion
Thr 19	-	insertion
Pro 20	Ser 18	conflict
Cys 22	Ser 20	conflict
Arg 23	Pro 21	conflict
Thr 24	Ala 22	conflict
Ser 49	Leu 47	conflict
Gln 50	Glu 48	conflict
Arg 95	His 93	conflict
Thr 101	Ile 99	conflict
Thr 102	Met 100	conflict
Gly 104	Ser 102	conflict
Ile 126	Val 124	conflict
Ile 132	Met 130	conflict
Ser 135	Ala 133	conflict
Lys 136	Arg 134	conflict
Arg 138	Pro 136	conflict
Lys 149	Arg 147	conflict
Lys 151	Arg 149	conflict
Thr 168	Tyr 166	conflict
Thr 169	Ala 167	conflict
Phe 176	-	insertion

U: 1 - 128 (UniProt: G1TSG1)

PDB	External Database	Details
Leu 18	Val 18	conflict
Gly 32	Arg 32	conflict
Ala 36	Glu 36	conflict
Phe 39	Ser 39	conflict
Gly 54	Arg 54	conflict
Val 60	Ala 60	conflict
Ser 62	Thr 62	conflict
Leu 63	Ile 63	conflict
Arg 97	His 97	conflict
Thr 106	Ser 106	conflict
Glu 126	Asp 126	conflict

k: 1 - 70 (UniProt: G1U001)

PDB	External Database	Details
Lys 24	Asn 24	conflict

AA: 1 - 295 (UniProt: G1TLT8)

PDB	External Database	Details
Thr 114	Ala 114	conflict

EE: 1 - 263 (UniProt: G1TK17)

PDB	External Database	Details
Gly 25	Ser 25	conflict
Arg 51	Lys 51	conflict
Thr 78	Ala 78	conflict
Val 156	Met 156	conflict

II: 1 - 208 (UniProt: G1TJW1)

PDB	External Database	Details
Arg 47	Gly 47	conflict

TT: 1 - 145 (UniProt: G1TN62)

PDB	External Database	Details
Gly 119	Trp 119	conflict

VV: 1 - 83 (UniProt: G1TM82)

PDB	External Database	Details
Asn 3	Ser 3	conflict
Asp 4	Asn 4	conflict
Gln 33	Pro 33	conflict
Phe 50	Ser 50	conflict
Ala 75	Ser 75	conflict
Asp 76	His 76	conflict
Lys 81	Gln 81	conflict

aa: 1 - 115 (UniProt: G1TFE8)

PDB	External Database	Details
Arg 28	Cys 28	conflict
Ala 56	Val 56	conflict
Arg 109	Pro 109	conflict

7: 1 - 120 (GenBank: X06789.1)

PDB	External Database	Details
U 2	N 2	conflict
C 36	N 36	conflict
U 102	N 102	conflict
U 112	N 112	conflict
U 114	N 114	conflict
U 119	C 119	conflict
U 120	N 120	conflict

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	81
Polymers	Total formula weight	3356184.0
Non-Polymers*	Number of molecules	286
Non-Polymers*	Total formula weight	7656.2
All*	Total formula weight	3363840.2

*Water molecules are not included.

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		Validation report (PDF)