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4V5Y: Crystal structure of the bacterial ribosome from Escherichia coli in complex with paromomycin and ribosome recycling factor (RRF)

PDB ID:

4V5Y Download

MMDB ID:

170992

PDB Deposition Date:

2007/6/19

Updated in MMDB:

2023/09

Experimental Method:

x-ray diffraction

Resolution:

4.45 Å

Source Organism:

Escherichia coli▼

Taxonomy

Molecule

Escherichia coli

AA, AC, AD, AE, AF, AG, AH, AI, AJ,
AK, AL, AM, AN, AO, AP, AQ, AR,
AS, AT, AB, AU, BA, BB, BI, BC,
BD, BK, BP, BE, BY, B0, B4, B1,
B3, BV, B2, BL, BM, BX, BH, BJ,
BN, BO, BQ, BS, BU, BF, BG, BR,
BT, BZ, BW, CA, CC, CD, CE, CF,
CG, CH, CI, CJ, CK, CL, CM, CN,
CO, CP, CQ, CR, CS, CT, CB, CU,
DA, DB, DI, DC, DD, DK, DP, DE,
DY, D0, D4, D1, D3, DV, D2, DL,
DM, DX, DH, DJ, DN, DO, DQ, DS,
DU, DF, DG, DR, DT, DZ, DW

Thermus thermophilus

B6, D6

Similar Structures:

Biological Unit for 4V5Y: 53-meric; determined by author

Molecular Components in 4V5Y
Label	Count	Molecule
Proteins (50 molecules)
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
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
AB	1	30S Ribosomal Protein S2
AU	1	30S Ribosomal Protein S21
BI	1	50S Ribosomal Protein L11
BC	1	50S Ribosomal Protein L2
BD	1	50S Ribosomal Protein L3
BK	1	50S Ribosomal Protein L14
BP	1	50S Ribosomal Protein L19
BE	1	50S Ribosomal Protein L4
BY	1	50S Ribosomal Protein L30
B0	1	50S Ribosomal Protein L32
B4	1	50S Ribosomal Protein L36
B1	1	50S Ribosomal Protein L33
B3	1	50S Ribosomal Protein L35
BV	1	50S Ribosomal Protein L25
B2	1	50S Ribosomal Protein L34
BL	1	50S Ribosomal Protein L15
BM	1	50S Ribosomal Protein L16
BX	1	50S Ribosomal Protein L29
BH	1	50S Ribosomal Protein L9
BJ	1	50S Ribosomal Protein L13
BN	1	50S Ribosomal Protein L17
BO	1	50S Ribosomal Protein L18
BQ	1	50S Ribosomal Protein L20
BS	1	50S Ribosomal Protein L22
BU	1	50S Ribosomal Protein L24
BF	1	50S Ribosomal Protein L5
BG	1	50S Ribosomal Protein L6
BR	1	50S Ribosomal Protein L21
BT	1	50S Ribosomal Protein L23
BZ	1	50S Ribosomal Protein L28
BW	1	50S Ribosomal Protein L27
B6	1	50S Ribosomal Protein RRF
Nucleotides(3 molecules)
AA	1	16S rRNA
BA	1	5S rRNA
BB	1	23S rRNA
Chemicals and Non-standard biopolymers (147 molecules)
1	144	MAGNESIUM ION
2	2	PAROMOMYCIN
3	1	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