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(-) Description

Title :  FK506-BINDING PROTEIN 2
 
Authors :  J. R. Walker, D. Neculai, T. Davis, C. Butler-Cole, F. Sicheri, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics Consortium (Sgc)
Date :  28 Mar 07  (Deposition) - 10 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Endoplasmic Reticulum, Isomerase, Polymorphism, Rotamase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, D. Neculai, T. Davis, C. Butler-Cole, F. Sicheri, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Structure Of Fk506-Binding Protein 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FK506-BINDING PROTEIN 2
    ChainsA, B, C, D
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28-LIC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 43-142
    GeneFKBP2, FKBP13
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEPTIDYL-PROLYL CIS-TRANS ISOMERASE, PPIASE, ROTAMASE, 13 KDA FKBP, FKBP-13

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:56 , VAL A:85 , ILE A:86 , TRP A:89 , TYR A:112 , HOH A:257BINDING SITE FOR RESIDUE PEG A 201
2AC2SOFTWARETYR B:56 , VAL B:85 , ILE B:86 , TRP B:89 , HOH B:225BINDING SITE FOR RESIDUE PEG B 201
3AC3SOFTWARETYR C:56 , PHE C:76 , VAL C:85 , ILE C:86 , TRP C:89 , TYR C:112 , HOH C:260BINDING SITE FOR RESIDUE PEG C 201
4AC4SOFTWARETYR D:56 , VAL D:85 , ILE D:86 , TRP D:89 , HOH D:232BINDING SITE FOR RESIDUE PEG D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PBC)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:118 -Pro A:119
2Pro B:118 -Pro B:119
3Pro C:118 -Pro C:119
4Pro D:118 -Pro D:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 8)

Asymmetric Unit (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006411A25TFKBP2_HUMANPolymorphism  ---A/B/C/DS42T
2UniProtVAR_006412C97YFKBP2_HUMANPolymorphism  ---A/B/C/DC97Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006411A25TFKBP2_HUMANPolymorphism  ---AS42T
2UniProtVAR_006412C97YFKBP2_HUMANPolymorphism  ---AC97Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006411A25TFKBP2_HUMANPolymorphism  ---BS42T
2UniProtVAR_006412C97YFKBP2_HUMANPolymorphism  ---BC97Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006411A25TFKBP2_HUMANPolymorphism  ---CS42T
2UniProtVAR_006412C97YFKBP2_HUMANPolymorphism  ---CC97Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006411A25TFKBP2_HUMANPolymorphism  ---DS42T
2UniProtVAR_006412C97YFKBP2_HUMANPolymorphism  ---DC97Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FKBP_PPIASEPS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.FKBP2_HUMAN49-137
 
 
 
  4A:49-137
B:49-137
C:49-137
D:49-137
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FKBP_PPIASEPS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.FKBP2_HUMAN49-137
 
 
 
  1A:49-137
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FKBP_PPIASEPS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.FKBP2_HUMAN49-137
 
 
 
  1-
B:49-137
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FKBP_PPIASEPS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.FKBP2_HUMAN49-137
 
 
 
  1-
-
C:49-137
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FKBP_PPIASEPS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.FKBP2_HUMAN49-137
 
 
 
  1-
-
-
D:49-137

(-) Exons   (5, 20)

Asymmetric Unit (5, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003945402ENSE00001518758chr11:64009588-6400968598FKBP2_HUMAN-00--
1.3ENST000003945403ENSE00001195899chr11:64009856-64010030175FKBP2_HUMAN1-57574A:41-57 (gaps)
B:41-57 (gaps)
C:41-57 (gaps)
D:41-57 (gaps)
34
34
34
34
1.4ENST000003945404ENSE00001195897chr11:64010671-64010783113FKBP2_HUMAN58-95384A:58-95
B:58-95
C:58-95
D:58-95
38
38
38
38
1.5ENST000003945405ENSE00001195893chr11:64010923-6401096947FKBP2_HUMAN95-111174A:95-111
B:95-111
C:95-111
D:95-111
17
17
17
17
1.6ENST000003945406ENSE00001195890chr11:64011313-6401134836FKBP2_HUMAN111-123134A:111-123
B:111-123
C:111-123
D:111-123
13
13
13
13
1.7ENST000003945407ENSE00001380157chr11:64011440-64011606167FKBP2_HUMAN123-142204A:123-140
B:123-139
C:123-140
D:123-139
18
17
18
17

(-) 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:100
 aligned with FKBP2_HUMAN | P26885 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:117
                                    33        43        53        63        73        83        93       103       113       123       133       
          FKBP2_HUMAN    24 GAEGKRKLQIGVKKRVDHCPIKSRKGDVLHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKIPGGATLVFEVELLKIERRT 140
               SCOP domains d2                 pbca_ A: automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------........eeeeeeeee.....eeee.......eeee......hhhhhh.........eeeeeehhhhh...............eeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) -T-----------------------------------------------------------------------Y------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------FKBP_PPIASE  PDB: A:49-137 UniProt: 49-137                                               --- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:41-57 (gaps)     Exon 1.4  PDB: A:58-95 UniProt: 58-95 ---------------Exon 1.6     ----------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5         -----------Exon 1.7           Transcript 1 (2)
                 2pbc A  41 GS-----------------PIKSRKGDVLHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKIPGGATLVFEVELLKIERRT 140
                             |       -        43        53        63        73        83        93       103       113       123       133       
                             |                43                                                                                                 
                            42                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with FKBP2_HUMAN | P26885 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:116
                                    33        43        53        63        73        83        93       103       113       123       133      
          FKBP2_HUMAN    24 GAEGKRKLQIGVKKRVDHCPIKSRKGDVLHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKIPGGATLVFEVELLKIERR 139
               SCOP domains d2                 pbcb_ B: automated matches                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------........eeeeeeeeee....eeee.......eeee......hhhhhhhh.......eeeeeehhhhh...............eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -T-----------------------------------------------------------------------Y------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------FKBP_PPIASE  PDB: B:49-137 UniProt: 49-137                                               -- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:41-57 (gaps)     Exon 1.4  PDB: B:58-95 UniProt: 58-95 ---------------Exon 1.6     ---------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5         -----------Exon 1.7          Transcript 1 (2)
                 2pbc B  41 GS-----------------PIKSRKGDVLHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKIPGGATLVFEVELLKIERR 139
                             |       -        43        53        63        73        83        93       103       113       123       133      
                            42                43                                                                                                

Chain C from PDB  Type:PROTEIN  Length:100
 aligned with FKBP2_HUMAN | P26885 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:117
                                    33        43        53        63        73        83        93       103       113       123       133       
          FKBP2_HUMAN    24 GAEGKRKLQIGVKKRVDHCPIKSRKGDVLHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKIPGGATLVFEVELLKIERRT 140
               SCOP domains d2                 pbcc_ C: automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------........eeeeeeeeee....eeee.......eeee......hhhhhhhh.......eeeeeehhhhh...............eeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) -T-----------------------------------------------------------------------Y------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------FKBP_PPIASE  PDB: C:49-137 UniProt: 49-137                                               --- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: C:41-57 (gaps)     Exon 1.4  PDB: C:58-95 UniProt: 58-95 ---------------Exon 1.6     ----------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5         -----------Exon 1.7           Transcript 1 (2)
                 2pbc C  41 GS-----------------PIKSRKGDVLHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKIPGGATLVFEVELLKIERRT 140
                             |       -        43        53        63        73        83        93       103       113       123       133       
                            42                43                                                                                                 

Chain D from PDB  Type:PROTEIN  Length:99
 aligned with FKBP2_HUMAN | P26885 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:116
                                    33        43        53        63        73        83        93       103       113       123       133      
          FKBP2_HUMAN    24 GAEGKRKLQIGVKKRVDHCPIKSRKGDVLHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKIPGGATLVFEVELLKIERR 139
               SCOP domains d2                 pbcd_ D: automated matches                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------FKBP_C-2pbcD01 D:43-134                                                                     ----- Pfam domains (1)
           Pfam domains (2) -------------------FKBP_C-2pbcD02 D:43-134                                                                     ----- Pfam domains (2)
           Pfam domains (3) -------------------FKBP_C-2pbcD03 D:43-134                                                                     ----- Pfam domains (3)
           Pfam domains (4) -------------------FKBP_C-2pbcD04 D:43-134                                                                     ----- Pfam domains (4)
         Sec.struct. author ..-----------------........eeeeeeeeee....eeee.......eeee......hhhhhhhh.......eeeeeehhhhh...............eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -T-----------------------------------------------------------------------Y------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------FKBP_PPIASE  PDB: D:49-137 UniProt: 49-137                                               -- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: D:41-57 (gaps)     Exon 1.4  PDB: D:58-95 UniProt: 58-95 ---------------Exon 1.6     ---------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5         -----------Exon 1.7          Transcript 1 (2)
                 2pbc D  41 GS-----------------PIKSRKGDVLHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKIPGGATLVFEVELLKIERR 139
                             |       -        43        53        63        73        83        93       103       113       123       133      
                            42                43                                                                                                

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PBC)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Family: FKBP_C (58)
1aFKBP_C-2pbcD01D:43-134
1bFKBP_C-2pbcD02D:43-134
1cFKBP_C-2pbcD03D:43-134
1dFKBP_C-2pbcD04D:43-134

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (FKBP2_HUMAN | P26885)
molecular function
    GO:0005528    FK506 binding    Interacting selectively and non-covalently with the 23-membered macrolide lactone FK506.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    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:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FKBP2_HUMAN | P268854nnr

(-) Related Entries Specified in the PDB File

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