1XMQ

Crystal Structure of t6A37-ASLLysUUU AAA-mRNA Bound to the Decoding Center


Domain Annotation: SCOP Classification SCOP Database (version: 2.0) Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpecies
Dd1xmqb_ Alpha and beta proteins (a/b) Flavodoxin-like Ribosomal protein S2 Ribosomal protein S2 Ribosomal protein S2 (Thermus thermophilus ) [TaxId: 274 ]
Fd1xmqd_ Alpha and beta proteins (a+b) Alpha-L RNA-binding motif Alpha-L RNA-binding motif Ribosomal protein S4 (bacteria) Ribosomal protein S4 (Thermus thermophilus ) [TaxId: 274 ]
Gd1xmqe1 Alpha and beta proteins (a+b) Ribosomal protein S5 domain 2-like Ribosomal protein S5 domain 2-like Translational machinery components Ribosomal protein S5, C-terminal domain (Thermus thermophilus ) [TaxId: 274 ]
Gd1xmqe2 Alpha and beta proteins (a+b) dsRBD-like dsRNA-binding domain-like Ribosomal S5 protein, N-terminal domain Ribosomal S5 protein, N-terminal domain (Thermus thermophilus ) [TaxId: 274 ]
Hd1xmqf_ Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S6 Ribosomal protein S6 Ribosomal protein S6 (Thermus thermophilus ) [TaxId: 274 ]
Id1xmqg_ All alpha proteins Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 (Thermus thermophilus ) [TaxId: 274 ]
Kd1xmqi_ Alpha and beta proteins (a+b) Ribosomal protein S5 domain 2-like Ribosomal protein S5 domain 2-like Translational machinery components Ribosomal protein S9 (Thermus thermophilus ) [TaxId: 274 ]
Ld1xmqj_ Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S10 Ribosomal protein S10 Ribosomal protein S10 (Thermus thermophilus ) [TaxId: 274 ]
Md1xmqk_ Alpha and beta proteins (a/b) Ribonuclease H-like motif Translational machinery components Ribosomal protein L18 and S11 Ribosomal protein S11 (Thermus thermophilus ) [TaxId: 274 ]
Od1xmqm_ All alpha proteins S13-like H2TH domain S13-like H2TH domain Ribosomal protein S13 Ribosomal protein S13 (Thermus thermophilus ) [TaxId: 274 ]
Qd1xmqo_ All alpha proteins S15/NS1 RNA-binding domain S15/NS1 RNA-binding domain Ribosomal protein S15 Ribosomal protein S15 (Thermus thermophilus ) [TaxId: 274 ]
Rd1xmqp_ Alpha and beta proteins (a+b) Ribosomal protein S16 Ribosomal protein S16 Ribosomal protein S16 Ribosomal protein S16 (Thermus thermophilus ) [TaxId: 274 ]
Td1xmqr_ All alpha proteins DNA/RNA-binding 3-helical bundle Ribosomal protein S18 Ribosomal protein S18 Ribosomal protein S18 (Thermus thermophilus ) [TaxId: 274 ]
Vd1xmqt_ All alpha proteins Spectrin repeat-like Ribosomal protein S20 Ribosomal protein S20 Ribosomal protein S20 (Thermus thermophilus ) [TaxId: 274 ]
Wd1xmqv_ Peptides Arg-rich RNA binding peptides 30S ribosomal protein THX 30S ribosomal protein THX 30S ribosomal protein THX (Thermus thermophilus ) [TaxId: 274 ]
Jd1xmqh_ Alpha and beta proteins (a+b) Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 (Thermus thermophilus ) [TaxId: 274 ]
Nd1xmql_ All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like Ribosomal protein S12 (Thermus thermophilus ) [TaxId: 274 ]
Pd1xmqn_ Small proteins Glucocorticoid receptor-like (DNA-binding domain) Glucocorticoid receptor-like (DNA-binding domain) Ribosomal protein S14 Ribosomal protein S14 (Thermus thermophilus ) [TaxId: 274 ]
Sd1xmqq_ All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like Ribosomal protein S17 (Thermus thermophilus ) [TaxId: 274 ]
Ud1xmqs_ Alpha and beta proteins (a+b) Ribosomal protein S19 Ribosomal protein S19 Ribosomal protein S19 Ribosomal protein S19 (Thermus thermophilus ) [TaxId: 274 ]
Ed1xmqc1 Alpha and beta proteins (a+b) Alpha-lytic protease prodomain-like Prokaryotic type KH domain (KH-domain type II) Prokaryotic type KH domain (KH-domain type II) Ribosomal protein S3 N-terminal domain (Thermus thermophilus ) [TaxId: 274 ]
Ed1xmqc2 Alpha and beta proteins (a+b) Ribosomal protein S3 C-terminal domain Ribosomal protein S3 C-terminal domain Ribosomal protein S3 C-terminal domain Ribosomal protein S3 C-terminal domain (Thermus thermophilus ) [TaxId: 274 ]
ChainDomainClassArchitectureTopologyHomology
D3.40.50.10490 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein
D3.40.50.10490 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein
D1.10.287.610 Mainly Alpha Orthogonal Bundle Helix Hairpins Helix hairpin bin
F1.10.1050.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41 Chain A, domain 1
F1.10.1050.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41 Chain A, domain 1
F3.10.290.10 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region Chain A
G3.30.160.20 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
G3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2
H3.30.70.60 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Ribosomal protein S6/Translation elongation factor EF1B
I1.10.455.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal protein S7/S5
K3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2
L3.30.70.600 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Ribosomal protein S10
M3.30.420.80 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5
O1.10.8.50 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3
O4.10.910.10 Few Secondary Structures Irregular 30s ribosomal protein s13 domain 2
Q1.10.287.10 Mainly Alpha Orthogonal Bundle Helix Hairpins S15/NS1, RNA-binding
R3.30.1320.10 Alpha Beta 2-Layer Sandwich S16 Ribosomal Protein Chain: A
T4.10.640.10 Few Secondary Structures Irregular 30s Ribosomal Protein S18 Ribosomal protein S18
V1.20.58.110 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase Chain G, domain 1
J3.30.1370.30 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8 Chain: A, domain 1
J3.30.1490.10 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1
N2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
P4.10.830.10 Few Secondary Structures Irregular 30s Ribosomal Protein S14 Chain N
S2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
U3.30.860.10 Alpha Beta 2-Layer Sandwich 30s Ribosomal Protein S19 Chain A
E3.30.300.20 Alpha Beta 2-Layer Sandwich GMP Synthetase Chain A, domain 3
E3.30.1140.32 Alpha Beta 2-Layer Sandwich Ribosomal protein S3 C-terminal domain Ribosomal protein S3, C-terminal domain

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
DPF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
FPF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
FPF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
GPF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
GPF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
HPF01250Ribosomal protein S6 (Ribosomal_S6)Ribosomal protein S6- Domain
IPF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
KPF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
LPF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20e- Family
MPF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
OPF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
QPF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
RPF00886Ribosomal protein S16 (Ribosomal_S16)Ribosomal protein S16- Family
TPF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
VPF01649Ribosomal protein S20 (Ribosomal_S20p)Ribosomal protein S20- Family
WPF1707030S ribosomal protein Thx (Thx)30S ribosomal protein Thx- Family
JPF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
NPF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PPF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
SPF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
UPF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
EPF07650KH domain (KH_2)KH domain- Domain
EPF00189Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C)Ribosomal protein S3, C-terminal domainThis family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.Domain

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A16s ribosomal RNAnone none none
XAnticodon RNAnone none none
B30S Ribosomal Protein S2
D30S Ribosomal Protein S4
E30S Ribosomal Protein S5
F30S Ribosomal Protein S6
G30S Ribosomal Protein S7
I30S Ribosomal Protein S9
J30S Ribosomal Protein S10
K30S Ribosomal Protein S11
M30S Ribosomal Protein S13
O30S Ribosomal Protein S15
P30S Ribosomal Protein S16
R30S Ribosomal Protein S18
T30S Ribosomal Protein S20
V30S Ribosomal Protein Thx
H30S Ribosomal Protein S8
L30S Ribosomal Protein S12
N30S Ribosomal Protein S14
Q30S Ribosomal Protein S17
WA-Site Messenger RNAnone none none
S30S Ribosomal Protein S19
C30S Ribosomal Protein S3