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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN SQUALENE SYNTHASE
 
Authors :  C. I. Liu, W. Y. Jeng, W. J. Chang, A. H. J. Wang
Date :  14 Oct 11  (Deposition) - 11 Apr 12  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Farnesyl-Diphosphate Farnesyltransferase, Head-To-Head Synthases, Cholesterol Biosynthesis, Oxidoreductase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. I. Liu, W. Y. Jeng, W. J. Chang, T. P. Ko, A. H. J. Wang
Binding Modes Of Zaragozic Acid A To Human Squalene Synthas And Staphylococcal Dehydrosqualene Synthase
J. Biol. Chem. V. 287 18750 2012
PubMed-ID: 22474324  |  Reference-DOI: 10.1074/JBC.M112.351254

(-) Compounds

Molecule 1 - SQUALENE SYNTHASE
    ChainsA, B
    EC Number2.5.1.21
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A
    Expression System StrainBL-21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 31-370
    GeneFDFT1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:98 , GLU A:343 , HIS A:347 , HOH A:455 , HOH A:466BINDING SITE FOR RESIDUE NI A 401
2AC2SOFTWAREHIS B:98 , GLU B:343 , HIS B:347 , HOH B:451BINDING SITE FOR RESIDUE NI B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011786K45RFDFT_HUMANPolymorphism11549147A/BK45R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011786K45RFDFT_HUMANPolymorphism11549147AK45R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011786K45RFDFT_HUMANPolymorphism11549147BK45R

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SQUALEN_PHYTOEN_SYN_1PS01044 Squalene and phytoene synthases signature 1.FDFT_HUMAN171-186
 
  2A:171-186
B:171-186
2SQUALEN_PHYTOEN_SYN_2PS01045 Squalene and phytoene synthases signature 2.FDFT_HUMAN207-232
 
  2A:207-232
B:207-232
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SQUALEN_PHYTOEN_SYN_1PS01044 Squalene and phytoene synthases signature 1.FDFT_HUMAN171-186
 
  1A:171-186
-
2SQUALEN_PHYTOEN_SYN_2PS01045 Squalene and phytoene synthases signature 2.FDFT_HUMAN207-232
 
  1A:207-232
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SQUALEN_PHYTOEN_SYN_1PS01044 Squalene and phytoene synthases signature 1.FDFT_HUMAN171-186
 
  1-
B:171-186
2SQUALEN_PHYTOEN_SYN_2PS01045 Squalene and phytoene synthases signature 2.FDFT_HUMAN207-232
 
  1-
B:207-232

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002205842aENSE00002161242chr8:11660120-11660440321FDFT_HUMAN1-33330--
1.5eENST000002205845eENSE00001087004chr8:11666303-1166640098FDFT_HUMAN34-66332A:35-66
B:36-66
32
31
1.6cENST000002205846cENSE00001087006chr8:11667176-11667359184FDFT_HUMAN66-127622A:66-127
B:66-127
62
62
1.7bENST000002205847bENSE00001087005chr8:11679259-11679387129FDFT_HUMAN128-170432A:128-170
B:128-170
43
43
1.8cENST000002205848cENSE00001087009chr8:11683533-11683724192FDFT_HUMAN171-234642A:171-234
B:171-234
64
64
1.9bENST000002205849bENSE00001087008chr8:11687753-11687929177FDFT_HUMAN235-293592A:235-293
B:235-293
59
59
1.10dENST0000022058410dENSE00001087003chr8:11689027-11689179153FDFT_HUMAN294-344512A:294-344
B:294-344
51
51
1.11jENST0000022058411jENSE00001323254chr8:11695897-11696818922FDFT_HUMAN345-417732A:345-369
B:345-369
25
25

(-) 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:335
 aligned with FDFT_HUMAN | P37268 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:335
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364     
           FDFT_HUMAN    35 SLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQ 369
               SCOP domains d3vjaa_ A: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------SQUALEN_PHYTOEN_--------------------SQUALEN_PHYTOEN_SYN_2     ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: A:35-66         -------------------------------------------------------------Exon 1.7b  PDB: A:128-170 UniProt: 128-170 Exon 1.8c  PDB: A:171-234 UniProt: 171-234                      Exon 1.9b  PDB: A:235-293 UniProt: 235-293                 Exon 1.10d  PDB: A:294-344 UniProt: 294-344        Exon 1.11j  PDB: A:345-36 Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.6c  PDB: A:66-127 UniProt: 66-127                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3vja A  35 SLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQ 369
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364     

Chain B from PDB  Type:PROTEIN  Length:334
 aligned with FDFT_HUMAN | P37268 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:334
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365    
           FDFT_HUMAN    36 LSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQ 369
               SCOP domains d3vjab_ B: automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------SQUALEN_PHYTOEN_--------------------SQUALEN_PHYTOEN_SYN_2     ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: B:36-66        -------------------------------------------------------------Exon 1.7b  PDB: B:128-170 UniProt: 128-170 Exon 1.8c  PDB: B:171-234 UniProt: 171-234                      Exon 1.9b  PDB: B:235-293 UniProt: 235-293                 Exon 1.10d  PDB: B:294-344 UniProt: 294-344        Exon 1.11j  PDB: B:345-36 Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.6c  PDB: B:66-127 UniProt: 66-127                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3vja B  36 LSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQ 369
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365    

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FDFT_HUMAN | P37268)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004310    farnesyl-diphosphate farnesyltransferase activity    Catalysis of the reaction: 2 farnesyl diphosphate = diphosphate + presqualene diphosphate.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0051996    squalene synthase activity    Catalysis of the reaction: presqualene diphosphate + NADPH = squalene + NADP+ + diphosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0006695    cholesterol biosynthetic process    The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0045338    farnesyl diphosphate metabolic process    The chemical reactions and pathways involving farnesyl diphosphate, an intermediate in carotenoid, sesquiterpene, squalene and sterol biosynthesis, as well as a substrate in protein farnesylation.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0008610    lipid biosynthetic process    The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016126    sterol biosynthetic process    The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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
        FDFT_HUMAN | P372681ezf 3asx 3lee 3q2z 3q30 3v66 3vj8 3vj9 3vjb 3vjc 3wc9 3wcd 3wcf 3wch 3wci 3wcj 3wcl 3wcm 3wef 3weg 3weh 3wei 3wej 3wek 3wsa

(-) Related Entries Specified in the PDB File

3vj8 3vj9 3vjb 3vjc 3vjd 3vje