Macromolecule Annotations for the Entities in PDB 2UXD

Domain Annotation: SCOP Classification SCOP Database (version: 1.75) Homepage

Chains Domain Info Class Fold Superfamily Family Domain Species
B7-241 d2uxdb1 Alpha and beta proteins (a/b) Flavodoxin-like Ribosomal protein S2 Ribosomal protein S2 Ribosomal protein S2 Thermus thermophilus [TaxId: 274]
D2-209 d2uxdd1 Alpha and beta proteins (a+b) Alpha-L RNA-binding motif Alpha-L RNA-binding motif Ribosomal protein S4 Ribosomal protein S4 Thermus thermophilus [TaxId: 274]
E5-154 d2uxde1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Small subunit 30S subunit Thermus thermophilus [TaxId: 274]
F1-101 d2uxdf1 Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S6 Ribosomal protein S6 Ribosomal protein S6 Thermus thermophilus [TaxId: 274]
G2-156 d2uxdg1 All alpha proteins Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 Thermus thermophilus [TaxId: 274]
H1-138 d2uxdh1 Alpha and beta proteins (a+b) Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 Thermus thermophilus [TaxId: 274]
I2-128 d2uxdi1 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]
J3-100 d2uxdj1 Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S10 Ribosomal protein S10 Ribosomal protein S10 Thermus thermophilus [TaxId: 274]
K11-126 d2uxdk1 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]
L5-128 d2uxdl1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
M2-126 d2uxdm1 All alpha proteins S13-like H2TH domain S13-like H2TH domain Ribosomal protein S13 Ribosomal protein S13 Thermus thermophilus [TaxId: 274]
N2-61 d2uxdn1 Small proteins Glucocorticoid receptor-like (DNA-binding domain) Glucocorticoid receptor-like (DNA-binding domain) Ribosomal protein S14 Ribosomal protein S14 Thermus thermophilus [TaxId: 274]
O2-89 d2uxdo1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
P1-83 d2uxdp1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
Q2-105 d2uxdq1 All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like Ribosomal protein S17 Thermus thermophilus [TaxId: 274]
R19-88 d2uxdr1 All alpha proteins DNA/RNA-binding 3-helical bundle Ribosomal protein S18 Ribosomal protein S18 Ribosomal protein S18 Thermus thermophilus [TaxId: 274]
S2-81 d2uxds1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
T8-106 d2uxdt1 All alpha proteins Spectrin repeat-like Ribosomal protein S20 Ribosomal protein S20 Ribosomal protein S20 Thermus thermophilus [TaxId: 274]
V2-25 d2uxdv1 Peptides Arg-rich RNA binding peptides 30S ribosomal protein THX 30S ribosomal protein THX 30S ribosomal protein THX Thermus thermophilus [TaxId: 274]

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Chains Domain Class Architecture Topology Homology
B1 2uxdB01 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein; domain 1
B2 2uxdB02 Mainly Alpha Orthogonal Bundle Helix Hairpins Helix hairpin bin
C1 2uxdC01 Alpha Beta 2-Layer Sandwich GMP Synthetase; Chain A, domain 3
C2 2uxdC02 Alpha Beta 2-Layer Sandwich Ribosomal protein S3 C-terminal domain
D1 2uxdD01 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41; Chain A, domain 1 Ribosomal Protein S4 Delta 41; Chain A, domain 1
D2 2uxdD02 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA- pckA Intergenic Region; Chain A Structural Genomics Hypothetical 15.5 Kd Protein In Mrca- pcka Intergenic Region; Chain
E1 2uxdE01 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
E2 2uxdE02 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
F 2uxdF00 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
G 2uxdG00 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal Protein S7;
H1 2uxdH01 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8; Chain: A, domain 1
H2 2uxdH02 Alpha Beta 2-Layer Sandwich Dna Ligase; domain 1
I 2uxdI00 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
J 2uxdJ00 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
K 2uxdK00 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase; domain 5
L 2uxdL00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
M1 2uxdM01 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein; domain 3
M2 2uxdM02 Few Secondary Structures Irregular 30s ribosomal protein s13; domain 2 30s ribosomal protein s13, domain 2
N 2uxdN00 Few Secondary Structures Irregular 30s Ribosomal Protein S14; Chain N 30s Ribosomal Protein S14; Chain N
O 2uxdO00 Mainly Alpha Orthogonal Bundle Helix Hairpins
P 2uxdP00 Alpha Beta 2-Layer Sandwich S16 Ribosomal Protein; Chain: A;
R 2uxdR00 Few Secondary Structures Irregular 30s Ribosomal Protein S18 30s Ribosomal Protein S18
S 2uxdS00 Alpha Beta 2-Layer Sandwich 30s Ribosomal Protein S19; Chain A 30s Ribosomal Protein S19; Chain A
T 2uxdT00 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase; Chain G, domain 1

Protein Family Annotation Pfam Database Homepage

Chains Pfam Accession Pfam Identifier Pfam Description Type Source
G PF00177 Ribosomal_S7 Ribosomal protein S7p/S5e Domain This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. PFAM PF00177
E PF03719 Ribosomal_S5_C Ribosomal protein S5, C-terminal domain Domain PFAM PF03719
T PF01649 Ribosomal_S20p Ribosomal protein S20 Family
J PF00338 Ribosomal_S10 Ribosomal protein S10p/S20e Family
I PF00380 Ribosomal_S9 Ribosomal protein S9/S16 Family
Q PF00366 Ribosomal_S17 Ribosomal protein S17 Domain PFAM PF00366
C PF00189 Ribosomal_S3_C Ribosomal protein S3, C-terminal domain Domain This 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. PFAM PF00189
E PF00333 Ribosomal_S5 Ribosomal protein S5, N-terminal domain Domain PFAM PF00333
R PF01084 Ribosomal_S18 Ribosomal protein S18 Family
S PF00203 Ribosomal_S19 Ribosomal protein S19 Domain PFAM PF00203
D PF00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain Family
F PF01250 Ribosomal_S6 Ribosomal protein S6 Domain PFAM PF01250
D PF01479 S4 S4 domain Domain 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. PFAM PF01479
H PF00410 Ribosomal_S8 Ribosomal protein S8 Domain PFAM PF00410
N PF00253 Ribosomal_S14 Ribosomal protein S14p/S29e Family
P PF00886 Ribosomal_S16 Ribosomal protein S16 Family
M PF00416 Ribosomal_S13 Ribosomal protein S13/S18 Family
K PF00411 Ribosomal_S11 Ribosomal protein S11 Family
C PF07650 KH_2 KH domain Domain PFAM PF07650
B PF00318 Ribosomal_S2 Ribosomal protein S2 Family
O PF00312 Ribosomal_S15 Ribosomal protein S15 Domain PFAM PF00312
L PF00164 Ribosom_S12_S23 Ribosomal protein S12/S23 Family

Gene Product Annotation Gene Ontology Consortium Homepage

Chains Polymer Molecular Function Biological Process Cellular Component
A 16S RIBOSOMAL RNA (2UXD:A)
  • none
  • none
  • none
B RIBOSOMAL PROTEIN S2 (2UXD:B)
C RIBOSOMAL PROTEIN S3 (2UXD:C)
D RIBOSOMAL PROTEIN S4 (2UXD:D)
E RIBOSOMAL PROTEIN S5 (2UXD:E)
F RIBOSOMAL PROTEIN S6 (2UXD:F)
G RIBOSOMAL PROTEIN S7 (2UXD:G)
H RIBOSOMAL PROTEIN S8 (2UXD:H)
I RIBOSOMAL PROTEIN S9 (2UXD:I)
J RIBOSOMAL PROTEIN S10 (2UXD:J)
K RIBOSOMAL PROTEIN S11 (2UXD:K)
L RIBOSOMAL PROTEIN S12 (2UXD:L)
M RIBOSOMAL PROTEIN S13 (2UXD:M)
N RIBOSOMAL PROTEIN S14 (2UXD:N)
O RIBOSOMAL PROTEIN S15 (2UXD:O)
P RIBOSOMAL PROTEIN S16 (2UXD:P)
Q RIBOSOMAL PROTEIN S17 (2UXD:Q)
R RIBOSOMAL PROTEIN S18 (2UXD:R)
S RIBOSOMAL PROTEIN S19 (2UXD:S)
T RIBOSOMAL PROTEIN S20 (2UXD:T)
V RIBOSOMAL PROTEIN THX (2UXD:V)
  • none
X ANTICODON STEM-LOOP OF TRANSFER RNA WITH ANTICODON CCCG (2UXD:X)
  • none
  • none
  • none
Y A-SITE MESSENGER RNA FRAGMENT CGGG (2UXD:Y)
  • none
  • none
  • none

Protein Modification Annotation

Type PDB Residue Nr. Description