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4V8N: The crystal structure of agmatidine tRNA-Ile2 bound to the 70S ribosome in the A and P site

PDB ID:

4V8N Download

MMDB ID:

171087

PDB Deposition Date:

2013/2/13

Updated in MMDB:

2021/03

Experimental Method:

x-ray diffraction

Resolution:

3.1 Å

Source Organism:

Thermus thermophilus HB8▼

Taxonomy	Molecule
Thermus thermophilus HB8	AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, B0, B1, B2, B3, B4, B5, B6, B7, B8, B9, BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BN, BO, BP, BQ, BR, BS, BT, BU, BV, BW, BX, BY, BZ, CA, CB, CC, CD, CE, CF, CG, CH, CI, CJ, CK, CL, CM, CN, CO, CP, CQ, CR, CS, CT, CU, D0, D1, D2, D3, D4, D5, D6, D7, D8, D9, DA, DB, DC, DD, DE, DF, DG, DH, DI, DJ, DN, DO, DP, DQ, DR, DS, DT, DU, DV, DW, DX, DY, DZ
Haloarcula marismortui	AV, AW, AY, CV, CW, CY
Escherichia coli	AX, CX

Similar Structures:

Biological Unit for 4V8N: 58-meric; determined by author

Molecular Components in 4V8N
Label	Count	Molecule
Proteins (51 molecules)
AB	1	30S Ribosomal Protein S2
AC	1	30S Ribosomal Protein S3
AD	1	30S Ribosomal Protein S4
AE	1	30S Ribosomal Protein S5
AF	1	30S Ribosomal Protein S6
AG	1	30S Ribosomal Protein S7
AH	1	30S Ribosomal Protein S8
AI	1	30S Ribosomal Protein S9
AJ	1	30S Ribosomal Protein S10
AK	1	30S Ribosomal Protein S11
AL	1	30S Ribosomal Protein S12
AM	1	30S Ribosomal Protein S13
AN	1	30S Ribosomal Protein S14 Type Z
AO	1	30S Ribosomal Protein S15
AP	1	30S Ribosomal Protein S16
AQ	1	30S Ribosomal Protein S17
AR	1	30S Ribosomal Protein S18
AS	1	30S Ribosomal Protein S19
AT	1	30S Ribosomal Protein S20
AU	1	30S Ribosomal Protein THX
B0	1	50S Ribosomal Protein L27
B1	1	50S Ribosomal Protein L28
B2	1	50S Ribosomal Protein L29
B3	1	50S Ribosomal Protein L30
B4	1	50S Ribosomal Protein L31
B5	1	50S Ribosomal Protein L32
B6	1	50S Ribosomal Protein L33
B7	1	50S Ribosomal Protein L34
B8	1	50S Ribosomal Protein L35
B9	1	50S Ribosomal Protein L36
BC	1	50S Ribosomal Protein L1
BD	1	50S Ribosomal Protein L2
BE	1	50S Ribosomal Protein L3
BF	1	50S Ribosomal Protein L4
BG	1	50S Ribosomal Protein L5
BH	1	50S Ribosomal Protein L6
BI	1	50S Ribosomal Protein L9
BJ	1	50S Ribosomal Protein L10
BN	1	50S Ribosomal Protein L13
BO	1	50S Ribosomal Protein L14
BP	1	50S Ribosomal Protein L15
BQ	1	50S Ribosomal Protein L16
BR	1	50S Ribosomal Protein L17
BS	1	50S Ribosomal Protein L18
BT	1	50S Ribosomal Protein L19
BU	1	50S Ribosomal Protein L20
BV	1	50S Ribosomal Protein L21
BW	1	50S Ribosomal Protein L22
BX	1	50S Ribosomal Protein L23
BY	1	50S Ribosomal Protein L24
BZ	1	50S Ribosomal Protein L25
Nucleotides(7 molecules)
AA	1	16S rRNA
AV AY	2	E-site tRNA Ile2 Agmatidine or P-site tRNA Ile2 Agmatidine
AW	1	A-site tRNA Ile2 Agmatidine
AX	1	mRNA
BA	1	23S Ribosomal RNA
BB	1	5S Ribosomal RNA
Chemicals and Non-standard biopolymers (2 molecules)
1	2	ZINC ION

* 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