Annotations | PepX: a structural database of protein-peptide complexes

Annotations

All protein-peptide complexes have been annotated with CATH, SCOP, PFAM and keywords from the PDB. A tag cloud of the 50 most occurring annotations in every category is presented below. The bigger the annotation, the more occurrent this annotation in the PepX database.

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SCOP Class

All alpha proteins All beta proteins Alpha and beta proteins (a+b) Alpha and beta proteins (a/b) Coiled coil proteins Designed proteins Membrane and cell surface proteins and peptides Multi-domain proteins (alpha and beta) Small proteins

SCOP Fold

6-bladed beta-propeller 7-bladed beta-propeller Acid proteases Acyl-CoA N-acyltransferases (Nat) alpha-alpha superhelix alpha/beta-Hydrolases beta-Grasp (ubiquitin-like) C-type lectin-like CI-2 family of serine protease inhibitors ClpS-like Common fold of diphtheria toxin/transcription factors/cytochrome f Concanavalin A-like lectins/glucanases Cyclin-like Cyclophilin-like Cysteine proteinases DHS-like NAD/FAD-binding domain DNA clamp EF Hand-like eIF4e-like Ferredoxin-like Flavodoxin-like Four-helical up-and-down bundle Heat shock protein 70kD (HSP70). peptide-binding domain Immunoglobulin-like beta-sandwich Inhibitor of apoptosis (IAP) repeat MHC antigen-recognition domain Nuclear receptor ligand-binding domain P-loop containing nucleoside triphosphate hydrolases Parallel coiled-coil PDZ domain-like Pentein. beta/alpha-propeller Periplasmic binding protein-like II PH domain-like barrel Phospholipase A2. PLA2 POZ domain Profilin-like Protein kinase-like (PK-like) RNase A-like RuvA C-terminal domain-like Serpins SH2-like SH3-like barrel SspB-like Stalk segment of viral fusion proteins Streptavidin-like Subdomain of clathrin and coatomer appendage domain Subtilisin-like SWIB/MDM2 domain Telomeric repeat binding factor (TRF) dimerisation domain Trypsin-like serine proteases

SCOP Superfamily

Acid proteases Acyl-CoA N-acyltransferases (Nat) alpha-catenin/vinculin-like ARM repeat ASF1-like Avidin/streptavidin Bacterial adhesins Bcl-2 inhibitors of programmed cell death C-type lectin-like CheY-like CI-2 family of serine protease inhibitors Cyclin-like Cyclophilin-like Cytochrome c oxidase subunit II-like. transmembrane region DNA clamp EF-hand eIF4e-like ENTH/VHS domain E set domains Heat shock protein 70kD (HSP70). peptide-binding domain Immunoglobulin Inhibitor of apoptosis (IAP) repeat Kelch motif Leucine zipper domain MHC antigen-recognition domain Nuclear receptor ligand-binding domain P-loop containing nucleoside triphosphate hydrolases PDZ domain-like Pentein Periplasmic binding protein-like II PH domain-like Phospholipase A2. PLA2 POZ domain Profilin (actin-binding protein) Protein kinase-like (PK-like) Protein prenylyltransferase Ribosomal protein L10-like RNase A-like Serpins SH2 domain SH3-domain SspB-like Subdomain of clathrin and coatomer appendage domain Subtilisin-like Telomeric repeat binding factor (TRF) dimerisation domain TPR-like Trimerization domain of TRAF Trypsin-like serine proteases Ubiquitin-like Virus ectodomain

SCOP Family

alpha-catenin/vinculin Armadillo repeat Avidin/streptavidin Bcl-2 inhibitors of programmed cell death C1 set domains (antibody constant domain-like) Calmodulin-like CheY-related CI-2 family of serine protease inhibitors Clathrin adaptor appendage. alpha and beta chain-specific domain Cyclin Cyclophilin (peptidylprolyl isomerase) DNA polymerase processivity factor Eukaryotic proteases Filamin repeat (rod domain) First domain of FERM G proteins Heat shock protein 70kD (HSP70). peptide-binding domain Inhibitor of apoptosis (IAP) repeat Kelch motif Leucine zipper domain MHC antigen-recognition domain N-acetyl transferase. NAT Nuclear receptor ligand-binding domain PDZ domain Pepsin-like Peptidylarginine deiminase Pad4. catalytic C-terminal domain Phosphotyrosine-binding domain (PTB) Pilus subunits Profilin (actin-binding protein) Protein kinases. catalytic subunit Protein prenylyltransferase Retinoblastoma tumor suppressor domains Retroviral protease (retropepsin) Ribonuclease A-like Serpins SH3-domain Stringent starvation protein B. SspB Subtilases Sulfatase-modifying factor-like Telomeric repeat binding factor (TRF) dimerisation domain Tetratricopeptide repeat (TPR) Translation initiation factor eIF4e Trimerization domain of TRAF Vertebrate phospholipase A2 VHS domain Viral cysteine protease of trypsin fold Viral proteases Virus ectodomain V set domains (antibody variable domain-like) WD40-repeat

CATH Class

Alpha Beta Few Secondary Structures Mainly Alpha Mainly Beta

CATH Topology

Alpha-Beta Plaits Aminopeptidase Antithrombin. Chain I. domain 2 Apoptosis. Tumor Necrosis Factor Receptor Associated Protein 2. Chain A Barwin-like endoglucanases Beta-Lactamase cAMP-dependent Protein Kinase. Chain A Cathepsin B. Chain A Cathepsin D. subunit A. domain 1 Class II Histocompatibility Antigen. M Beta Chain. Chain B. domain 1 Cyclin A. domain 1 Cyclophilin Four Helix Bundle (Hemerythrin (Met). subunit A) Helicase. Ruva Protein. domain 3 Immunoglobulin-like Inhibitor Of Apoptosis Protein (2mihbC-IAP-1). Chain A Jelly Rolls Leucine-rich Repeat Variant Lipocalin MDM2 Methylamine Dehydrogenase. Chain H Murine Class I Major Histocompatibility Complex. H2-DB. Chain A. domain 1 Neuraminidase P-30 Protein paralog of FGE (formylglycine-generating enzyme) Pdz3 Domain PH-domain like Phospholipase A2 Phosphorylase Kinase. domain 1 Porin Proliferating Cell Nuclear Antigen Recoverin. domain 1 Retinoid X Receptor Ribosomal Protein L30. Chain A. RNA Cap. Translation Initiation Factor Eif4e Rossmann fold Serine Threonine Protein Phosphatase 5. Tetratricopeptide repeat Severin SH3 type barrels. SHC Adaptor Protein Single alpha-helices involved in coiled-coils or other helix-helix interfaces Substrate Binding Domain Of DNAk. Chain A. domain 1 TATA-Binding Protein Thrombin. subunit H TIM Barrel Trypsin Inhibitor V. Chain A Ubiquitin-like (UB roll) vbs2 fragment of talin Vitelline Membrane Outer Layer Protein I. subunit A Wheat Germ Agglutinin (Isolectin 2). domain 1

CATH Superfamily

Acid Proteases Actin. Chain A. domain 4 Adenoviral Proteinase. Chain A Antithrombin. subunit I. domain 2 Apoptosis. Tumor Necrosis Factor Receptor Associated Protein 2. Chain A Apoptosis Regulator Bcl-x cAMP-dependent Protein Kinase. Chain A Class II Histocompatibility Antigen. M Beta Chain. Chain B. domain 1 Cupredoxins - Cyclophilin Cysteine proteinases DNA helicase RuvA subunit. C-terminal domain EF-hand Galactose-binding domain-like HIV Envelope Protein Gp120. Chain G Immunoglobulins Inhibitor Of Apoptosis Protein (2mihbC-IAP-1). Chain A Kelch-like ech-associated protein 1 Leucine-rich Repeat Variant MDM2 Murine Class I Major Histocompatibility Complex. H2-DB. subunit A. domain 1 P-30 Protein P-loop containing nucleotide triphosphate hydrolases paralog of FGE (formylglycine-generating enzyme) Periplasmic binding protein-like II Phosphatidylinositol 3-kinase Catalytic Subunit. Chain A. domain 1 Phospholipase A2 Phosphorylase Kinase. domain 1 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) Porin Potassium Channel Kv1.1. Chain A Protein Inhibitor Of Neuronal Nitric Oxide Synthase. Retinoid X Receptor Ricin (A Subunit). domain 2 RNA Cap. Translation Initiation Factor Eif4e Severin SH3 Domains SHC Adaptor Protein Stringent starvation protein B. SspB Substrate Binding Domain Of DNAk. Chain A. domain 1 TATA-Binding Protein Telomeric repeat binding factor (TRF) dimerisation domain TPP-binding domain Trypsin-like serine proteases Trypsin Inhibitor V. subunit A Vaccinia Virus protein VP39 Vinculin head like domains winged helix YVTN repeat-like/Quinoprotein amine dehydrogenase Zinc/RING finger domain. C3HC4 (zinc finger)