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or a peptidyl-tRNA analog

PDB ID:	5DGV Download
MMDB ID:	171191
PDB Deposition Date:	2015/8/28
Updated in MMDB:	2021/02
Experimental Method:	x-ray diffraction
Resolution:	3.1 Å
Source Organism:	Saccharomyces cerevisiae S288C
Similar Structures:

Biological Unit for 5DGV: 84-meric; determined by software (PISA)

Molecular Components in 5DGV
Label	Count	Molecule
Proteins (79 molecules)
s0	1	40S Ribosomal Protein S0-a
s1	1	40S Ribosomal Protein S1-a
s2	1	40S Ribosomal Protein S2
s3	1	40S Ribosomal Protein S3
s4	1	40S Ribosomal Protein S4-a
s5	1	40S Ribosomal Protein S5
s6	1	40S Ribosomal Protein S6-a
s7	1	40S Ribosomal Protein S7-a
s8	1	40S Ribosomal Protein S8-a
s9	1	40S Ribosomal Protein S9-a
c0	1	40S Ribosomal Protein S10-a
c1	1	40S Ribosomal Protein S11-a
c2	1	40S Ribosomal Protein S12
c3	1	40S Ribosomal Protein S13
c4	1	40S Ribosomal Protein S14-a
c5	1	40S Ribosomal Protein S15
c6	1	40S Ribosomal Protein S16-a
c7	1	40S Ribosomal Protein S17-a
c8	1	40S Ribosomal Protein S18-a
c9	1	40S Ribosomal Protein S19-a
d0	1	40S Ribosomal Protein S20
d1	1	40S Ribosomal Protein S21-a
d2	1	40S Ribosomal Protein S22-a
d3	1	40S Ribosomal Protein S23-a
d4	1	40S Ribosomal Protein S24-a
d5	1	40S Ribosomal Protein S25-a
d6	1	40S Ribosomal Protein S26-b
d7	1	40S Ribosomal Protein S27-a
d8	1	40S Ribosomal Protein S28-a
d9	1	40S Ribosomal Protein S29-a
e1	1	Ubiquitin-40s Ribosomal Protein S31
sR	1	Guanine Nucleotide-binding Protein Subunit Beta-like Protein
sM	1	Suppressor Protein Stm1
l2	1	60S Ribosomal Protein L2-a
l3	1	60S Ribosomal Protein L3
l4	1	60S Ribosomal Protein L4-a
l5	1	60S Ribosomal Protein L5
l6	1	60S Ribosomal Protein L6-a
l7	1	60S Ribosomal Protein L7-a
l8	1	60S Ribosomal Protein L8-a (El8)
l9	1	60S Ribosomal Protein L9-a
m0	1	60S Ribosomal Protein L10
m1	1	60S Ribosomal Protein L11-b
m3	1	60S Ribosomal Protein L13-a
m4	1	60S Ribosomal Protein L14-a
m5	1	60S Ribosomal Protein L15-a
m6	1	60S Ribosomal Protein L16-a
m7	1	60S Ribosomal Protein L17-a
m8	1	60S Ribosomal Protein L18-a
m9	1	60S Ribosomal Protein L19-a
n0	1	60S Ribosomal Protein L20-a
n1	1	60S Ribosomal Protein L21-a
n2	1	60S Ribosomal Protein L22-a
n3	1	60S Ribosomal Protein L23-a
n4	1	60S Ribosomal Protein L24-a
n5	1	60S Ribosomal Protein L25
n6	1	60S Ribosomal Protein L26-a
n7	1	60S Ribosomal Protein L27-a
n8	1	60S Ribosomal Protein L28
n9	1	60S Ribosomal Protein L29
o0	1	60S Ribosomal Protein L30
o1	1	60S Ribosomal Protein L31-a
o2	1	60S Ribosomal Protein L32
o3	1	60S Ribosomal Protein L33-a
o4	1	60S Ribosomal Protein L34-a
o5	1	60S Ribosomal Protein L35-a
o6	1	60S Ribosomal Protein L36-a
o7	1	60S Ribosomal Protein L37-a
o8	1	60S Ribosomal Protein L38
o9	1	60S Ribosomal Protein L39
q0	1	Ubiquitin-60s Ribosomal Protein L40
q1	1	60S Ribosomal Protein L41-a
q2	1	60S Ribosomal Protein L42-a
q3	1	60S Ribosomal Protein L43-a
e0	1	40S Ribosomal Protein S30-a
m2	1	60S Ribosomal Protein L12-a (Ul11)
p0	1	60S Acidic Ribosomal Protein P0
p1	1	60S Ribosomal Protein P1 Alpha/p2 Beta
p2	1	60S Ribosomal Protein P1 Alpha/p2 Beta
Nucleotides(4 molecules)
6	1	Saccharomyces Cerevisiae S288c Rdn37-1 Miscrna
5	1	25S Ribosomal RNA
7	1	5S Ribosomal RNA
8	1	5.8s Ribosomal RNA
Chemicals and Non-standard biopolymers (11 molecules)
D	1	DNA (5'-R(CPCP(8AN)(Pro)*(Pro))-3')
1	8	ZINC ION
2	1	SPARSOMYCIN
3	1	MAGNESIUM 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