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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CASPASE-1 WITH A NATURALLY-OCCURRING ASN263->SER SUBSTITUTION IN COMPLEX WITH 3-[2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)-PROPIONYLAMINO]-4-OXO-PENTANOIC ACID (Z-VAD-FMK)
 
Authors :  A. Rosen-Wolff, J. Roesler, M. J. Romanowski
Date :  19 May 08  (Deposition) - 02 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Catalytic Domain, Naturally-Occurring Mutation, Apoptosis, Hydrolase, Protease, Thiol Protease, Zymogen, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Rosen-Wolff, M. J. Romanowski, L. Ritter, S. Flecks, N. Quoos, J. Gramatt, C. Petzold, H. D. Nguyen, M. Gahr, J. Roesler
Mutated, Structurally Altered Caspase-1 With Decreased Enzymatic And Increased Rip2-Meditated Inflammatory Activit Leads To A New Type Of Periodic Fever (Ice Fever).
To Be Published 2008
PubMed: search

(-) Compounds

Molecule 1 - CASPASE-1
    ChainsA
    EC Number3.4.22.36
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSET B
    Expression System StrainBL21(DE3) CODON+
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCASPASE-1 SUBUNIT P20
    GeneCASP1, IL1BC, IL1BCE
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCASP-1, INTERLEUKIN-1 BETA CONVERTASE, IL-1BC, IL-1 BETA- CONVERTING ENZYME, ICE, INTERLEUKIN-1 BETA-CONVERTING ENZYME, P45, CASPASE-1 SUBUNIT P20, CASPASE-1 SUBUNIT P10
 
Molecule 2 - CASPASE-1 PRECURSOR
    ChainsB
    EC Number3.4.22.36
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSET B
    Expression System StrainBL21(DE3) CODON+
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCASPASE-1 SUBUNIT P10
    GeneCASP1, IL1BC, IL1BCE
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCASP-1, INTERLEUKIN-1 BETA CONVERTASE, IL-1BC, IL-1 BETA- CONVERTING ENZYME, ICE, INTERLEUKIN-1 BETA-CONVERTING ENZYME, P45, CASPASE-1 SUBUNIT P20, CASPASE-1 SUBUNIT P10
 
Molecule 3 - N-[(BENZYLOXY)CARBONYL]-L-VALYL-N-[(2S)-1-CARBOXY-4-FLUORO- 3-OXOBUTAN-2-YL]-L-ALANINAMIDE
    ChainsC
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (2x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CF01Mod. Amino AcidFLUOROMETHANE
2PHQ1Mod. Amino AcidBENZYL CHLOROCARBONATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CF02Mod. Amino AcidFLUOROMETHANE
2PHQ2Mod. Amino AcidBENZYL CHLOROCARBONATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:179 , HIS A:237 , GLY A:238 , GLN A:283 , CYS A:285 , HOH B:168 , SER B:339 , TRP B:340 , ARG B:341 , HIS B:342 , ARG B:383 , HOH C:400BINDING SITE FOR CHAIN C OF N-[(BENZYLOXY) CARBONYL]-L-VALYL-N-[(2S)-1-CARBOXY-4-FLUORO- 3-OXOBUTAN-2-YL]-L- ALANINAMIDE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D6H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D6H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D6H)

(-) PROSITE Motifs  (4, 4)

Asymmetric Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.CASP1_HUMAN161-289  1A:161-289
2CASPASE_HISPS01121 Caspase family histidine active site.CASP1_HUMAN224-238  1A:224-238
3CASPASE_CYSPS01122 Caspase family cysteine active site.CASP1_HUMAN276-287  1A:276-287
4CASPASE_P10PS50207 Caspase family p10 domain profile.CASP1_HUMAN317-402  1B:317-402
Biological Unit 1 (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.CASP1_HUMAN161-289  2A:161-289
2CASPASE_HISPS01121 Caspase family histidine active site.CASP1_HUMAN224-238  2A:224-238
3CASPASE_CYSPS01122 Caspase family cysteine active site.CASP1_HUMAN276-287  2A:276-287
4CASPASE_P10PS50207 Caspase family p10 domain profile.CASP1_HUMAN317-402  2B:317-402

(-) Exons   (0, 0)

(no "Exon" information available for 3D6H)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:166
 aligned with CASP1_HUMAN | P29466 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:166
                                   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      
          CASP1_HUMAN   132 NVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPRRTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKVIIIQACRGDSPGVVWFKD 297
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...............eeeeee...........hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeee.......ee..........eehhhhhhhhh....hhhhh...eeeeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------CASPASE_P20  PDB: A:161-289 UniProt: 161-289                                                                                     -------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------CASPASE_HIS    -------------------------------------CASPASE_CYS ---------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d6h A 132 NVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPRRTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFSMLNTKNCPSLKDKPKVIIIQACRGDSPGVVWFKD 297
                                   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      

Chain B from PDB  Type:PROTEIN  Length:88
 aligned with CASP1_HUMAN | P29466 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:88
                                   326       336       346       356       366       376       386       396        
          CASP1_HUMAN   317 AIKKAHIEKDFIAFCSSTPDNVSWRHPTMGSVFIGRLIEHMQEYACSCDVEEIFRKVRFSFEQPDGRAQMPTTERVTLTRCFYLFPGH 404
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee.........ee...eehhhhhhhhhhhhhh...hhhhhhhhhhhh...........eee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CASPASE_P10  PDB: B:317-402 UniProt: 317-402                                          -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3d6h B 317 AIKKAHIEKDFIAFCSSTPDNVSWRHPTMGSVFIGRLIEHMQEYACSCDVEEIFRKVRFSFEQPDGRAQMPTTERVTLTRCFYLFPGH 404
                                   326       336       346       356       366       376       386       396        

Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3d6h C   1 xVADx   5
                            |   |
                            1-PHQ
                                5-CF0

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3D6H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D6H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D6H)

(-) Gene Ontology  (40, 40)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CASP1_HUMAN | P29466)
molecular function
    GO:0008656    cysteine-type endopeptidase activator activity involved in apoptotic process    Increases the rate of proteolysis catalyzed by a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0097153    cysteine-type endopeptidase activity involved in apoptotic process    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile, and contributing to the apoptotic process.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0071310    cellular response to organic substance    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0032611    interleukin-1 beta production    The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0060081    membrane hyperpolarization    The process in which membrane potential increases with respect to its steady-state potential, usually from negative potential to a more negative potential. For example, during the repolarization phase of an action potential the membrane potential often becomes more negative or hyperpolarized before returning to the steady-state resting potential.
    GO:0051882    mitochondrial depolarization    The process in which the potential difference across the mitochondrial membrane is reduced from its steady state level.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0050715    positive regulation of cytokine secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell.
    GO:0050717    positive regulation of interleukin-1 alpha secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 alpha from a cell.
    GO:0050718    positive regulation of interleukin-1 beta secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
    GO:0097300    programmed necrotic cell death    A necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0070269    pyroptosis    A caspase-1-dependent cell death subroutine that is associated with the generation of pyrogenic mediators such as IL-1beta and IL-18.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0033198    response to ATP    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ATP (adenosine 5'-triphosphate) stimulus.
    GO:0009617    response to bacterium    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0097169    AIM2 inflammasome complex    A protein complex that consists of AIM2, ASC, and caspase-1. AIM2 is a member of the HN-200 protein family that appears to be the sensor of cytosolic double-stranded DNA.
    GO:0072557    IPAF inflammasome complex    A protein complex that consists of three components, IPAF, NAIP and caspase-1, and includes among its functions the sensing of flagellin derived from Legionella pneumophila, Salmonella typhimurium, Pseudomonas aeruginosa and Shigella flexneri.
    GO:0072558    NLRP1 inflammasome complex    A protein complex that consists of two components, NLRP1 (NALP1) and caspase-1 or caspase-5. The exact mechanisms of NLRP1 activation remain obscure, but potassium ion efflux appears to be essential.
    GO:0072559    NLRP3 inflammasome complex    A protein complex that consists of three components, NLRP3 (NALP3), PYCARD and caspase-1. It is activated upon exposure to whole pathogens, as well as a number of structurally diverse pathogen- and danger-associated molecular patterns (PAMPs and DAMPs) and environmental irritants. Whole pathogens demonstrated to activate the NLRP3 inflammasome complex include the fungi Candida albicans and Saccharomyces cerevisiae, bacteria that produce pore-forming toxins, including Listeria monocytogenes and Staphylococcus aureus, and viruses such as Sendai virus, adenovirus, and influenza virus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CASP1_HUMAN | P294661bmq 1ibc 1ice 1rwk 1rwm 1rwn 1rwo 1rwp 1rwv 1rww 1rwx 1sc1 1sc3 1sc4 2fqq 2h48 2h4w 2h4y 2h51 2h54 2hbq 2hbr 2hby 2hbz 3d6f 3d6m 3e4c 3ns7 5fna

(-) Related Entries Specified in the PDB File

1sc3 3d6f 3d6m