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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PTS1 COMPLEXED TO THE TPR REGION OF HUMAN PEX5
 
Authors :  G. J. Gatto Jr. , B. V. Geisbrecht, S. J. Gould, J. M. Berg
Date :  18 Jul 00  (Deposition) - 06 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (2x)
Biol. Unit 4:  A,B,C,D  (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Protein-Peptide Complex, Tetratricopeptide Repeat, Tpr, Helical Repeat, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. J. Gatto Jr. , B. V. Geisbrecht, S. J. Gould, J. M. Berg
Peroxisomal Targeting Signal-1 Recognition By The Tpr Domains Of Human Pex5.
Nat. Struct. Biol. V. 7 1091 2000
PubMed-ID: 11101887  |  Reference-DOI: 10.1038/81930
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7
    Expression System Taxid562
    FragmentC-TERMINAL TPR REGION
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEROXISMORE RECEPTOR 1, PTS1-BP, PEROXIN-5, PTS1 RECEPTOR
 
Molecule 2 - PTS1-CONTAINING PEPTIDE
    ChainsC, D
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D
Biological Unit 3 (2x)ABCD
Biological Unit 4 (1x)ABCD
Biological Unit 5 (1x)A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1FCH)

(-) Sites  (0, 0)

(no "Site" information available for 1FCH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FCH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FCH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007543N526KPEX5_HUMANDisease (PBD2B)61752138A/BN489K
2UniProtVAR_031328S600WPEX5_HUMANDisease (PBD2B)  ---A/BS563W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007543N526KPEX5_HUMANDisease (PBD2B)61752138AN489K
2UniProtVAR_031328S600WPEX5_HUMANDisease (PBD2B)  ---AS563W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007543N526KPEX5_HUMANDisease (PBD2B)61752138BN489K
2UniProtVAR_031328S600WPEX5_HUMANDisease (PBD2B)  ---BS563W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007543N526KPEX5_HUMANDisease (PBD2B)61752138A/BN489K
2UniProtVAR_031328S600WPEX5_HUMANDisease (PBD2B)  ---A/BS563W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007543N526KPEX5_HUMANDisease (PBD2B)61752138A/BN489K
2UniProtVAR_031328S600WPEX5_HUMANDisease (PBD2B)  ---A/BS563W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 5 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007543N526KPEX5_HUMANDisease (PBD2B)61752138A/BN489K
2UniProtVAR_031328S600WPEX5_HUMANDisease (PBD2B)  ---A/BS563W

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

(-) PROSITE Motifs  (2, 12)

Asymmetric Unit (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.PEX5_HUMAN335-368
 
369-402
 
488-521
 
522-555
 
556-589
 
  10A:298-331
B:298-331
A:332-365
B:332-365
A:451-484
B:451-484
A:485-518
B:485-518
A:519-552
B:519-552
2TPR_REGIONPS50293 TPR repeat region circular profile.PEX5_HUMAN335-589
 
  2A:298-552
B:298-552
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.PEX5_HUMAN335-368
 
369-402
 
488-521
 
522-555
 
556-589
 
  5A:298-331
-
A:332-365
-
A:451-484
-
A:485-518
-
A:519-552
-
2TPR_REGIONPS50293 TPR repeat region circular profile.PEX5_HUMAN335-589
 
  1A:298-552
-
Biological Unit 2 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.PEX5_HUMAN335-368
 
369-402
 
488-521
 
522-555
 
556-589
 
  5-
B:298-331
-
B:332-365
-
B:451-484
-
B:485-518
-
B:519-552
2TPR_REGIONPS50293 TPR repeat region circular profile.PEX5_HUMAN335-589
 
  1-
B:298-552
Biological Unit 3 (2, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.PEX5_HUMAN335-368
 
369-402
 
488-521
 
522-555
 
556-589
 
  20A:298-331
B:298-331
A:332-365
B:332-365
A:451-484
B:451-484
A:485-518
B:485-518
A:519-552
B:519-552
2TPR_REGIONPS50293 TPR repeat region circular profile.PEX5_HUMAN335-589
 
  4A:298-552
B:298-552
Biological Unit 4 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.PEX5_HUMAN335-368
 
369-402
 
488-521
 
522-555
 
556-589
 
  10A:298-331
B:298-331
A:332-365
B:332-365
A:451-484
B:451-484
A:485-518
B:485-518
A:519-552
B:519-552
2TPR_REGIONPS50293 TPR repeat region circular profile.PEX5_HUMAN335-589
 
  2A:298-552
B:298-552
Biological Unit 5 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.PEX5_HUMAN335-368
 
369-402
 
488-521
 
522-555
 
556-589
 
  10A:298-331
B:298-331
A:332-365
B:332-365
A:451-484
B:451-484
A:485-518
B:485-518
A:519-552
B:519-552
2TPR_REGIONPS50293 TPR repeat region circular profile.PEX5_HUMAN335-589
 
  2A:298-552
B:298-552

(-) Exons   (0, 0)

(no "Exon" information available for 1FCH)

(-) 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:302
 aligned with PEX5_HUMAN | P50542 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:323
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636   
           PEX5_HUMAN   317 SATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACETLRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARDLSTLLTMFGLPQ 639
               SCOP domains d1fcha_ A: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1fchA00 A:280-602  [code=1.25.40.10, no name defined]                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..............hhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhh.---------------..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K-------------------------------------------------------------------------W--------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------TPR_REGION  PDB: A:298-552 UniProt: 335-589                                                                                                                                                                                                                    -------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------TPR  PDB: A:298-331               TPR  PDB: A:332-365               -------------------------------------------------------------------------------------TPR  PDB: A:451-484               TPR  PDB: A:485-518               TPR  PDB: A:519-552               -------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fch A 280 SATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVT---------------RILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKS------GGAMSENIWSTLRLALSMLGQSDAYGAADARDLSTLLTMFGLPQ 602
                                   289       299       309       319       329       339       349       359       369       379       389       399    |    -         -|      429       439       449       459       469       479       489       499       509       519       529       539       549  |    559       569       579       589       599   
                                                                                                                                                      404             420                                                                                                                                 552    559                                           

Chain B from PDB  Type:PROTEIN  Length:297
 aligned with PEX5_HUMAN | P50542 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:318
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631        
           PEX5_HUMAN   322 KGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACETLRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARDLSTLLTMFGLPQ 639
               SCOP domains d1fchb_ B: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1fchB00 B:285-602  [code=1.25.40.10, no name defined]                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..--------------..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.-------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K-------------------------------------------------------------------------W--------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------TPR_REGION  PDB: B:298-552 UniProt: 335-589                                                                                                                                                                                                                    -------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------TPR  PDB: B:298-331               TPR  PDB: B:332-365               -------------------------------------------------------------------------------------TPR  PDB: B:451-484               TPR  PDB: B:485-518               TPR  PDB: B:519-552               -------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fch B 285 KGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTP--------------RILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKS-------GAMSENIWSTLRLALSMLGQSDAYGAADARDLSTLLTMFGLPQ 602
                                   294       304       314       324       334       344       354       364       374       384       394       404|        -     | 424       434       444       454       464       474       484       494       504       514       524       534       544       | -     | 564       574       584       594        
                                                                                                                                                  405            420                                                                                                                                 552     560                                          

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
                 1fch C   1 YQSKL   5

Chain D 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
                 1fch D   1 YQSKL   5

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FCH)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PEX5_HUMAN | P50542)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0005052    peroxisome matrix targeting signal-1 binding    Interacting selectively and non-covalently with a type 1 peroxisome targeting signal, a tripeptide with the consensus sequence (S/A/C)-(K/R/H)-L.
    GO:0000268    peroxisome targeting sequence binding    Interacting selectively and non-covalently with a peroxisomal targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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).
    GO:0031267    small GTPase binding    Interacting selectively and non-covalently with a small monomeric GTPase.
biological process
    GO:1901094    negative regulation of protein homotetramerization    Any process that stops, prevents or reduces the frequency, rate or extent of protein homotetramerization.
    GO:0016558    protein import into peroxisome matrix    The import of proteins into the peroxisomal matrix. A peroxisome targeting signal (PTS) binds to a soluble receptor protein in the cytosol, and the resulting complex then binds to a receptor protein in the peroxisome membrane and is imported. The cargo protein is then released into the peroxisome matrix.
    GO:0016560    protein import into peroxisome matrix, docking    The process in which a complex formed of a peroxisome targeting sequence (PTS) receptor bound to a PTS-bearing protein docks with translocation machinery in the peroxisomal membrane.
    GO:0016561    protein import into peroxisome matrix, translocation    The process in which proteins are moved across the peroxisomal membrane into the matrix. It is likely that the peroxisome targeting sequence receptor remains associated with cargo proteins during translocation.
    GO:0045046    protein import into peroxisome membrane    The targeting of proteins into the peroxisomal membrane. The process is not well understood, but both signals and mechanism differ from those involved in peroxisomal matrix protein import.
    GO:0006625    protein targeting to peroxisome    The process of directing proteins towards the peroxisome, usually using signals contained within the protein.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    GO:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

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        PEX5_HUMAN | P505422c0l 2c0m 2j9q 2w84 3r9a 4bxu 4kxk 4kyo

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