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8UD6: Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.70A resolution

PDB ID:

8UD6 Download

MMDB ID:

243111

PDB Deposition Date:

2023/9/28

Updated in MMDB:

2024/03

Experimental Method:

x-ray diffraction

Resolution:

2.7 Å

Source Organism:

Thermus thermophilus HB8▼

Taxonomy	Molecule
Thermus thermophilus HB8	1A, 1B, 1D, 1E, 1F, 1G, 1H, 1I, 1N, 1O, 1P, 1Q, 1R, 1S, 1T, 1U, 1V, 1W, 1X, 1Y, 1Z, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1a, 1b, 1c, 1d, 1e, 1f, 1g, 1h, 1i, 1j, 1k, 1l, 1m, 1n, 1o, 1p, 1q, 1r, 1s, 1t, 1u, 2A, 2B, 2D, 2E, 2F, 2G, 2H, 2I, 2N, 2O, 2P, 2Q, 2R, 2S, 2T, 2U, 2V, 2W, 2X, 2Y, 2Z, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 2a, 2b, 2c, 2d, 2e, 2f, 2g, 2h, 2i, 2j, 2k, 2l, 2m, 2n, 2o, 2p, 2q, 2r, 2s, 2t, 2u
Tequatrovirus T4	1v, 2v
Escherichia coli	1w, 1x, 1y, 2w, 2x, 2y

Similar Structures:

Biological Unit for 8UD6: 112-meric; determined by author

Molecular Components in 8UD6
Label	Count	Molecule
Proteins (98 molecules)
1D 2D	2	50S Ribosomal Protein L2
1E 2E	2	50S Ribosomal Protein L3
1F 2F	2	50S Ribosomal Protein L4
1G 2G	2	50S Ribosomal Protein L5
1H 2H	2	50S Ribosomal Protein L6
1I 2I	2	50S Ribosomal Protein L9
1N 2N	2	50S Ribosomal Protein L13
1O 2O	2	50S Ribosomal Protein L14
1P 2P	2	50S Ribosomal Protein L15
1Q 2Q	2	50S Ribosomal Protein L16
1R 2R	2	50S Ribosomal Protein L17
1S 2S	2	50S Ribosomal Protein L18
1T 2T	2	50S Ribosomal Protein L19
1U 2U	2	50S Ribosomal Protein L20
1V 2V	2	50S Ribosomal Protein L21
1W 2W	2	50S Ribosomal Protein L22
1X 2X	2	50S Ribosomal Protein L23
1Y 2Y	2	50S Ribosomal Protein L24
1Z 2Z	2	50S Ribosomal Protein L25
10 20	2	50S Ribosomal Protein L27
11 21	2	50S Ribosomal Protein L28
12 22	2	50S Ribosomal Protein L29
13 23	2	50S Ribosomal Protein L30
14 24	2	50S Ribosomal Protein L31
15 25	2	50S Ribosomal Protein L32
16 26	2	50S Ribosomal Protein L33
17 27	2	50S Ribosomal Protein L34
18 28	2	50S Ribosomal Protein L35
19 29	2	50S Ribosomal Protein L36
1b 2b	2	30S Ribosomal Protein S2
1c 2c	2	30S Ribosomal Protein S3
1d 2d	2	30S Ribosomal Protein S4
1e 2e	2	30S Ribosomal Protein S5
1f 2f	2	30S Ribosomal Protein S6
1g 2g	2	30S Ribosomal Protein S7
1h 2h	2	30S Ribosomal Protein S8
1i 2i	2	30S Ribosomal Protein S9
1j 2j	2	30S Ribosomal Protein S10
1k 2k	2	30S Ribosomal Protein S11
1l 2l	2	30S Ribosomal Protein S12
1m 2m	2	30S Ribosomal Protein S13
1n 2n	2	30S Ribosomal Protein S14 Type Z
1o 2o	2	30S Ribosomal Protein S15
1p 2p	2	30S Ribosomal Protein S16
1q 2q	2	30S Ribosomal Protein S17
1r 2r	2	30S Ribosomal Protein S18
1s 2s	2	30S Ribosomal Protein S19
1t 2t	2	30S Ribosomal Protein S20
1u 2u	2	30S Ribosomal Protein THX
Nucleotides(14 molecules)
1A 2A	2	23S Ribosomal RNA
1B 2B	2	5S Ribosomal RNA
1a 2a	2	16S Ribosomal RNA
1v 2v	2	Mf-mrna
1w 1y 2w 2y	4	A- and E-site Deacylated Trnaphe
1x 2x	2	P-site Aminoacyl-trna Fmet-trnamet
Chemicals and Non-standard biopolymers (2589 molecules)
1	2571	MAGNESIUM ION
2	2	POTASSIUM ION
3	2	(4S,5aS,8S,8aR)-4-(2-methylpropyl)-N-[(1R,5Z,7R,8R,9R,10R,11S,12R)-10,11,12-trihydroxy-7-methyl-13-oxa-2-thiabicyclo[7.3.1]tridec-5-en-8-yl]octahydro-2H-oxepino[2,3-c]pyrrole-8-carboxamide (non-preferred name)
4	12	ZINC ION
5	2	IRON/SULFUR CLUSTER

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303