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(-) Description

Title :  STRUCTURE OF RECOMBINANT HUMAN CYTOCHROME C
 
Authors :  B. S. Rajagopal, J. A. R. Worrall, M. A. Hough
Date :  20 Nov 12  (Deposition) - 23 Oct 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
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 :  Electron Transport, Respiration, Apoptosis, Electron Transfer (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. S. Rajagopal, A. N. Edzuma, M. A. Hough, K. L. I. M. Blundell, V. E. Kagan, A. A. Kapralov, L. A. Fraser, J. N. Butt, G. G. Silkstone, M. T. Wilson, D. A. Svistunenko, J. A. R. Worrall
The Hydrogen Peroxide Induced Radical Behaviour In Human Cytochrome C Phospholipid Complexes: Implications For The Enhanced Pro-Apoptotic Activity Of The G41S Mutant
Biochem. J. V. 456 441 2013
PubMed-ID: 24099549  |  Reference-DOI: 10.1042/BJ20130758

(-) Compounds

Molecule 1 - CYTOCHROME C
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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
1HEC4Ligand/IonHEME C
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:13 , CYS A:14 , CYS A:17 , HIS A:18 , THR A:28 , GLY A:29 , PRO A:30 , THR A:40 , GLY A:41 , TYR A:46 , TYR A:48 , THR A:49 , ASN A:52 , TRP A:59 , TYR A:67 , LEU A:68 , THR A:78 , LYS A:79 , MET A:80 , ILE A:81 , PHE A:82 , ILE A:85 , HOH A:2055 , LYS B:55BINDING SITE FOR RESIDUE HEC A 105
2AC2SOFTWARELYS B:13 , CYS B:14 , CYS B:17 , HIS B:18 , THR B:28 , GLY B:29 , PRO B:30 , THR B:40 , GLY B:41 , TYR B:46 , TYR B:48 , THR B:49 , ASN B:52 , TRP B:59 , TYR B:67 , LEU B:68 , THR B:78 , LYS B:79 , MET B:80 , LEU B:94 , HOH B:2025 , HOH B:2029BINDING SITE FOR RESIDUE HEC B 105
3AC3SOFTWARELYS C:13 , CYS C:14 , CYS C:17 , HIS C:18 , THR C:28 , PRO C:30 , THR C:40 , GLY C:41 , TYR C:46 , TYR C:48 , THR C:49 , ASN C:52 , TRP C:59 , TYR C:67 , LEU C:68 , THR C:78 , LYS C:79 , MET C:80 , LEU C:94 , HOH C:2020 , HOH C:2025 , LYS D:55BINDING SITE FOR RESIDUE HEC C 105
4AC4SOFTWARELYS A:55 , LYS D:13 , CYS D:14 , CYS D:17 , HIS D:18 , THR D:28 , PRO D:30 , THR D:40 , GLY D:41 , TYR D:46 , TYR D:48 , THR D:49 , ASN D:52 , TRP D:59 , TYR D:67 , LEU D:68 , THR D:78 , LYS D:79 , MET D:80 , ILE D:85 , LEU D:94 , HOH D:2034BINDING SITE FOR RESIDUE HEC D 105

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 12)

Asymmetric Unit (3, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_044450G42SCYC_HUMANDisease (THC4)121918552A/B/C/DG41S
2UniProtVAR_048850K56RCYC_HUMANPolymorphism11548795A/B/C/DK55R
3UniProtVAR_002204M66LCYC_HUMANPolymorphism  ---A/B/C/DM65L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_044450G42SCYC_HUMANDisease (THC4)121918552AG41S
2UniProtVAR_048850K56RCYC_HUMANPolymorphism11548795AK55R
3UniProtVAR_002204M66LCYC_HUMANPolymorphism  ---AM65L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_044450G42SCYC_HUMANDisease (THC4)121918552BG41S
2UniProtVAR_048850K56RCYC_HUMANPolymorphism11548795BK55R
3UniProtVAR_002204M66LCYC_HUMANPolymorphism  ---BM65L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_044450G42SCYC_HUMANDisease (THC4)121918552CG41S
2UniProtVAR_048850K56RCYC_HUMANPolymorphism11548795CK55R
3UniProtVAR_002204M66LCYC_HUMANPolymorphism  ---CM65L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_044450G42SCYC_HUMANDisease (THC4)121918552DG41S
2UniProtVAR_048850K56RCYC_HUMANPolymorphism11548795DK55R
3UniProtVAR_002204M66LCYC_HUMANPolymorphism  ---DM65L

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HUMAN2-103
 
 
 
  4A:1-102
B:1-102
C:1-102
D:1-102
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HUMAN2-103
 
 
 
  1A:1-102
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HUMAN2-103
 
 
 
  1-
B:1-102
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HUMAN2-103
 
 
 
  1-
-
C:1-102
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HUMAN2-103
 
 
 
  1-
-
-
D:1-102

(-) Exons   (2, 8)

Asymmetric Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003057861aENSE00001286932chr7:25164980-25164819162CYC_HUMAN-00--
1.3ENST000003057863ENSE00001147465chr7:25163746-25163570177CYC_HUMAN1-57574A:1-56
B:1-56
C:1-56
D:1-56
56
56
56
56
1.4dENST000003057864dENSE00001207041chr7:25163468-251597103759CYC_HUMAN57-105494A:56-104
B:56-104
C:56-104
D:56-104
49
49
49
49

(-) 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:104
 aligned with CYC_HUMAN | P99999 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
            CYC_HUMAN     2 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 105
               SCOP domains d3zcfa_ A: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------S-------------R---------L--------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: A:1-102 UniProt: 2-103                                                                     -- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-56 UniProt: 1-57 [INCOMPLETE]        ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.4d  PDB: A:56-104 UniProt: 57-105          Transcript 1 (2)
                 3zcf A   1 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 104
                                    10        20        30        40        50        60        70        80        90       100    

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with CYC_HUMAN | P99999 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
            CYC_HUMAN     2 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 105
               SCOP domains d3zcfb_ B: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------S-------------R---------L--------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:1-102 UniProt: 2-103                                                                     -- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:1-56 UniProt: 1-57 [INCOMPLETE]        ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.4d  PDB: B:56-104 UniProt: 57-105          Transcript 1 (2)
                 3zcf B   1 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 104
                                    10        20        30        40        50        60        70        80        90       100    

Chain C from PDB  Type:PROTEIN  Length:104
 aligned with CYC_HUMAN | P99999 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
            CYC_HUMAN     2 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 105
               SCOP domains d3zcfc_ C: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------S-------------R---------L--------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: C:1-102 UniProt: 2-103                                                                     -- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: C:1-56 UniProt: 1-57 [INCOMPLETE]        ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.4d  PDB: C:56-104 UniProt: 57-105          Transcript 1 (2)
                 3zcf C   1 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 104
                                    10        20        30        40        50        60        70        80        90       100    

Chain D from PDB  Type:PROTEIN  Length:104
 aligned with CYC_HUMAN | P99999 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
            CYC_HUMAN     2 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 105
               SCOP domains d3zcfd_ D: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..................................hhhhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------S-------------R---------L--------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: D:1-102 UniProt: 2-103                                                                     -- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: D:1-56 UniProt: 1-57 [INCOMPLETE]        ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.4d  PDB: D:56-104 UniProt: 57-105          Transcript 1 (2)
                 3zcf D   1 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 104
                                    10        20        30        40        50        60        70        80        90       100    

   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 3ZCF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CYC_HUMAN | P99999)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0045155    electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity    Enables the directed movement of electrons from the CoQH2-cytochrome c reductase complex and the cytochrome c oxidase complex.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004722    protein serine/threonine phosphatase activity    Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
biological process
    GO:0008635    activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process and is mediated by cytochrome c.
    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:0045333    cellular respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
    GO:0097193    intrinsic apoptotic signaling pathway    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).
    GO:0006123    mitochondrial electron transport, cytochrome c to oxygen    The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
    GO:0006122    mitochondrial electron transport, ubiquinol to cytochrome c    The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    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:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0000302    response to reactive oxygen species    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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
cellular component
    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:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    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.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0000159    protein phosphatase type 2A complex    A protein complex that has protein serine/threonine phosphatase activity that is polycation-stimulated (PCS), being directly stimulated by protamine, polylysine, or histone H1; it constitutes a subclass of several enzymes activated by different histones and polylysine, and consists of catalytic, scaffolding, and regulatory subunits. The catalytic and scaffolding subunits form the core enzyme, and the holoenzyme also includes the regulatory subunit.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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 Related Entries

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

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        CYC_HUMAN | P999991j3s 2n3y 2n9i 2n9j 3nwv 3zoo 5exq

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