Macromolecule Annotations for the Entities in PDB 2VQF

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

Chains Domain Info Class Fold Superfamily Family Domain Species
B7-241 d2vqfb1 Alpha and beta proteins (a/b) Flavodoxin-like Ribosomal protein S2 Ribosomal protein S2 Ribosomal protein S2 Thermus thermophilus [TaxId: 274]
D2-209 d2vqfd1 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 d2vqfe1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Small subunit 30S subunit Thermus thermophilus [TaxId: 274]
F1-101 d2vqff1 Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S6 Ribosomal protein S6 Ribosomal protein S6 Thermus thermophilus [TaxId: 274]
G2-156 d2vqfg1 All alpha proteins Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 Thermus thermophilus [TaxId: 274]
H1-138 d2vqfh1 Alpha and beta proteins (a+b) Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 Thermus thermophilus [TaxId: 274]
I2-128 d2vqfi1 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 d2vqfj1 Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S10 Ribosomal protein S10 Ribosomal protein S10 Thermus thermophilus [TaxId: 274]
K11-126 d2vqfk1 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 d2vqfl1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
M2-126 d2vqfm1 All alpha proteins S13-like H2TH domain S13-like H2TH domain Ribosomal protein S13 Ribosomal protein S13 Thermus thermophilus [TaxId: 274]
N2-61 d2vqfn1 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 d2vqfo1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
P1-83 d2vqfp1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
Q2-105 d2vqfq1 All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like Ribosomal protein S17 Thermus thermophilus [TaxId: 274]
R16-88 d2vqfr1 All alpha proteins DNA/RNA-binding 3-helical bundle Ribosomal protein S18 Ribosomal protein S18 Ribosomal protein S18 Thermus thermophilus [TaxId: 274]
S2-81 d2vqfs1 Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
T8-106 d2vqft1 All alpha proteins Spectrin repeat-like Ribosomal protein S20 Ribosomal protein S20 Ribosomal protein S20 Thermus thermophilus [TaxId: 274]
U2-25 d2vqfu1 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 2vqfB01 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein; domain 1
B2 2vqfB02 Mainly Alpha Orthogonal Bundle Helix Hairpins Helix hairpin bin
C1 2vqfC01 Alpha Beta 2-Layer Sandwich GMP Synthetase; Chain A, domain 3
C2 2vqfC02 Alpha Beta 2-Layer Sandwich Ribosomal protein S3 C-terminal domain
D1 2vqfD01 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41; Chain A, domain 1 Ribosomal Protein S4 Delta 41; Chain A, domain 1
D2 2vqfD02 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 2vqfE01 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
E2 2vqfE02 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
F 2vqfF00 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
G 2vqfG00 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal Protein S7;
H1 2vqfH01 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8; Chain: A, domain 1
H2 2vqfH02 Alpha Beta 2-Layer Sandwich Dna Ligase; domain 1
I 2vqfI00 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
J 2vqfJ00 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
K 2vqfK00 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase; domain 5
L 2vqfL00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
M1 2vqfM01 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein; domain 3
M2 2vqfM02 Few Secondary Structures Irregular 30s ribosomal protein s13; domain 2 30s ribosomal protein s13, domain 2
N 2vqfN00 Few Secondary Structures Irregular 30s Ribosomal Protein S14; Chain N 30s Ribosomal Protein S14; Chain N
O 2vqfO00 Mainly Alpha Orthogonal Bundle Helix Hairpins
P 2vqfP00 Alpha Beta 2-Layer Sandwich S16 Ribosomal Protein; Chain: A;
R 2vqfR00 Few Secondary Structures Irregular 30s Ribosomal Protein S18 30s Ribosomal Protein S18
S 2vqfS00 Alpha Beta 2-Layer Sandwich 30s Ribosomal Protein S19; Chain A 30s Ribosomal Protein S19; Chain A
T 2vqfT00 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
R PF01084 Ribosomal_S18 Ribosomal protein S18 Family
Q PF00366 Ribosomal_S17 Ribosomal protein S17 Domain PFAM PF00366
L PF00164 Ribosom_S12_S23 Ribosomal protein S12/S23 Family
K PF00411 Ribosomal_S11 Ribosomal protein S11 Family
J PF00338 Ribosomal_S10 Ribosomal protein S10p/S20e Family
T PF01649 Ribosomal_S20p Ribosomal protein S20 Family
F PF01250 Ribosomal_S6 Ribosomal protein S6 Domain PFAM PF01250
I PF00380 Ribosomal_S9 Ribosomal protein S9/S16 Family
E PF03719 Ribosomal_S5_C Ribosomal protein S5, C-terminal domain Domain PFAM PF03719
N PF00253 Ribosomal_S14 Ribosomal protein S14p/S29e Family
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
D PF00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain Family
P PF00886 Ribosomal_S16 Ribosomal protein S16 Family
H PF00410 Ribosomal_S8 Ribosomal protein S8 Domain PFAM PF00410
M PF00416 Ribosomal_S13 Ribosomal protein S13/S18 Family
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
B PF00318 Ribosomal_S2 Ribosomal protein S2 Family
C PF07650 KH_2 KH domain Domain PFAM PF07650
E PF00333 Ribosomal_S5 Ribosomal protein S5, N-terminal domain Domain PFAM PF00333
S PF00203 Ribosomal_S19 Ribosomal protein S19 Domain PFAM PF00203
O PF00312 Ribosomal_S15 Ribosomal protein S15 Domain PFAM PF00312
G PF00177 Ribosomal_S7 Ribosomal protein S7p/S5e Domain This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. PFAM PF00177

Gene Product Annotation Gene Ontology Consortium Homepage

Chains Polymer Molecular Function Biological Process Cellular Component
A 16S RRNA (2VQF:A)
  • none
  • none
  • none
B 30S RIBOSOMAL PROTEIN S2 (2VQF:B)
C 30S RIBOSOMAL PROTEIN S3 (2VQF:C)
D 30S RIBOSOMAL PROTEIN S4 (2VQF:D)
E 30S RIBOSOMAL PROTEIN S5 (2VQF:E)
F 30S RIBOSOMAL PROTEIN S6 (2VQF:F)
G 30S RIBOSOMAL PROTEIN S7 (2VQF:G)
H 30S RIBOSOMAL PROTEIN S8 (2VQF:H)
I 30S RIBOSOMAL PROTEIN S9 (2VQF:I)
J 30S RIBOSOMAL PROTEIN S10 (2VQF:J)
K 30S RIBOSOMAL PROTEIN S11 (2VQF:K)
L 30S RIBOSOMAL PROTEIN S12 (2VQF:L)
M 30S RIBOSOMAL PROTEIN S13 (2VQF:M)
N 30S RIBOSOMAL PROTEIN S14 TYPE Z (2VQF:N)
O 30S RIBOSOMAL PROTEIN S15 (2VQF:O)
P 30S RIBOSOMAL PROTEIN S16 (2VQF:P)
Q 30S RIBOSOMAL PROTEIN S17 (2VQF:Q)
R 30S RIBOSOMAL PROTEIN S18 (2VQF:R)
S 30S RIBOSOMAL PROTEIN S19 (2VQF:S)
T 30S RIBOSOMAL PROTEIN S20 (2VQF:T)
U 30S RIBOSOMAL PROTEIN THX (2VQF:U)
  • none
X 5'-R(*UP*UP*GP*AP*AP*AP)-3' (2VQF:X)
  • none
  • none
  • none
Y 5'-R(*GP*CP*AP*UP*GP*CP*U*TM2P*AP*AP*AP *AP*CP*AP*UP*GP*C)- 3' (2VQF:Y)
  • none
  • none
  • none