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(-) Description

Title :  STRUCTURE OF PSEUDOMONAS NAUTICA CYTOCHROME C552, BY MAD METHOD
 
Authors :  K. Brown, D. Nurizzo, C. Cambillau
Date :  03 Aug 98  (Deposition) - 22 Jul 99  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Electron Transport, Pseudomonas Nautica, X Ray Structure, Multiwavelength Anomalous Dispersion, Heme, Cytochrome C (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Brown, D. Nurizzo, S. Besson, W. Shepard, J. Moura, I. Moura, M. Tegoni, C. Cambillau
Mad Structure Of Pseudomonas Nautica Dimeric Cytochrome C55 Mimicks The C4 Dihemic Cytochrome Domain Association.
J. Mol. Biol. V. 289 1017 1999
PubMed-ID: 10369779  |  Reference-DOI: 10.1006/JMBI.1999.2838

(-) Compounds

Molecule 1 - CYTOCHROME C552
    AtccINSTITUT PASTEUR CULTURE COLLECTION 617/1.85
    Cellular LocationPERIPLASM
    ChainsA, B, C, D, E, F, G, H
    CollectionINSTITUT PASTEUR CULTURE COLLECTION 617/1.85
    Organism ScientificMARINOBACTER HYDROCARBONOCLASTICUS
    Organism Taxid2743
    Other DetailsC HEME IN EACH MONOMER LINKED BY CYS 14 AND 17 AND HIS 18 AND MET 60 AS AXIAL LIGANDS
    Strain617

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)AB      
Biological Unit 2 (1x)  CD    
Biological Unit 3 (1x)    EF  
Biological Unit 4 (1x)      GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2HEC8Ligand/IonHEME C
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2HEC2Ligand/IonHEME C
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2HEC2Ligand/IonHEME C
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2HEC2Ligand/IonHEME C
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2HEC2Ligand/IonHEME C

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:13 , CYS A:14 , CYS A:17 , HIS A:18 , TYR A:29 , PRO A:30 , LEU A:32 , TYR A:39 , LEU A:44 , TYR A:47 , ARG A:52 , GLN A:56 , MET A:60 , GLN A:63 , HOH A:204 , HOH A:212 , HOH A:242 , TYR B:39 , ARG B:52 , HEC B:200 , GLN E:56 , VAL E:59BINDING SITE FOR RESIDUE HEC A 200
02AC2SOFTWARETYR A:39 , ARG A:52 , HEC A:200 , HOH A:202 , VAL B:13 , CYS B:14 , CYS B:17 , HIS B:18 , TYR B:29 , PRO B:30 , LEU B:32 , TYR B:39 , LEU B:44 , TYR B:47 , ARG B:52 , GLN B:56 , MET B:60 , GLN B:63 , HOH B:201 , HOH B:218BINDING SITE FOR RESIDUE HEC B 200
03AC3SOFTWAREVAL C:13 , CYS C:14 , CYS C:17 , HIS C:18 , TYR C:29 , PRO C:30 , LEU C:32 , TYR C:39 , LEU C:44 , TYR C:47 , ARG C:52 , GLN C:56 , ALA C:57 , MET C:60 , GLN C:63 , HOH C:204 , HOH C:213 , TYR D:39 , ARG D:52 , HEC D:200 , TYR H:29BINDING SITE FOR RESIDUE HEC C 200
04AC4SOFTWARETYR C:39 , ARG C:52 , HEC C:200 , VAL D:13 , CYS D:14 , CYS D:17 , HIS D:18 , TYR D:29 , PRO D:30 , LEU D:32 , TYR D:39 , TYR D:47 , ARG D:52 , GLN D:56 , ALA D:57 , VAL D:59 , MET D:60 , GLN D:63 , LEU D:75 , HOH D:207 , HOH D:229 , HOH D:239BINDING SITE FOR RESIDUE HEC D 200
05AC5SOFTWARETYR A:29 , VAL E:13 , CYS E:14 , CYS E:17 , HIS E:18 , TYR E:29 , PRO E:30 , LEU E:32 , TYR E:39 , TYR E:47 , ARG E:52 , MET E:60 , GLN E:63 , HOH E:203 , HOH E:217 , HOH E:224 , TYR F:39 , ARG F:52 , HEC F:200 , HOH F:204BINDING SITE FOR RESIDUE HEC E 200
06AC6SOFTWARETYR E:39 , ARG E:52 , HEC E:200 , VAL F:13 , CYS F:14 , CYS F:17 , HIS F:18 , TYR F:29 , PRO F:30 , LEU F:32 , TYR F:39 , LEU F:40 , TYR F:47 , ARG F:52 , GLN F:56 , ALA F:57 , MET F:60 , GLN F:63 , HOH F:206 , HOH F:207 , HOH F:234BINDING SITE FOR RESIDUE HEC F 200
07AC7SOFTWAREVAL G:13 , CYS G:14 , CYS G:17 , HIS G:18 , TYR G:29 , PRO G:30 , LEU G:32 , TYR G:39 , LEU G:44 , TYR G:47 , ARG G:52 , GLN G:56 , VAL G:59 , MET G:60 , HOH G:201 , HOH G:277 , HOH G:299 , TYR H:39 , ARG H:52 , HEC H:200BINDING SITE FOR RESIDUE HEC G 200
08AC8SOFTWAREGLN C:56 , VAL C:59 , TYR G:39 , ARG G:52 , HEC G:200 , VAL H:13 , CYS H:14 , CYS H:17 , HIS H:18 , TYR H:29 , PRO H:30 , LEU H:32 , TYR H:39 , LEU H:44 , TYR H:47 , ARG H:52 , GLN H:56 , ALA H:57 , MET H:60 , GLN H:63 , HOH H:201 , HOH H:223 , HOH H:224BINDING SITE FOR RESIDUE HEC H 200
09AC9SOFTWARELYS E:36 , GLU E:37 , HOH E:208 , PRO F:27BINDING SITE FOR RESIDUE GOL E 201
10BC1SOFTWAREHOH E:256 , GLN F:53 , GLY F:54 , PRO F:58 , HOH F:285 , LYS G:48 , ALA G:49BINDING SITE FOR RESIDUE GOL F 201
11BC2SOFTWARETHR F:65 , HOH F:241 , LYS G:8 , ALA G:12 , GLN G:20 , TYR G:78BINDING SITE FOR RESIDUE GOL F 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CNO)

(-) PROSITE Motifs  (1, 8)

Asymmetric Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CY552_MARHY2-83
 
 
 
 
 
 
 
  8A:2-83
B:2-83
C:2-83
D:2-83
E:2-83
F:2-83
G:2-83
H:2-83
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CY552_MARHY2-83
 
 
 
 
 
 
 
  2A:2-83
B:2-83
-
-
-
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CY552_MARHY2-83
 
 
 
 
 
 
 
  2-
-
C:2-83
D:2-83
-
-
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CY552_MARHY2-83
 
 
 
 
 
 
 
  2-
-
-
-
E:2-83
F:2-83
-
-
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CY552_MARHY2-83
 
 
 
 
 
 
 
  2-
-
-
-
-
-
G:2-83
H:2-83

(-) Exons   (0, 0)

(no "Exon" information available for 1CNO)

(-) 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:86
 aligned with CY552_MARHY | P82903 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           CY552_MARHY    1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASLPADG 86
               SCOP domains d1cnoa_ A: Cytochrome c552                                                             SCOP domains
               CATH domains 1cnoA00 A:1-86 Cytochrome c                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhh..................hhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: A:2-83 UniProt: 2-83                                                   --- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  1cno A  1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASNPAAA 86
                                    10        20        30        40        50        60        70        80      

Chain B from PDB  Type:PROTEIN  Length:86
 aligned with CY552_MARHY | P82903 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           CY552_MARHY    1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASLPADG 86
               SCOP domains d1cnob_ B: Cytochrome c552                                                             SCOP domains
               CATH domains 1cnoB00 B:1-86 Cytochrome c                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..................hhhhhhhhhhhh........hhhhhhh.....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: B:2-83 UniProt: 2-83                                                   --- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  1cno B  1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASNPAAA 86
                                    10        20        30        40        50        60        70        80      

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with CY552_MARHY | P82903 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           CY552_MARHY    1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASLPADG 86
               SCOP domains d1cnoc_ C: Cytochrome c552                                                             SCOP domains
               CATH domains 1cnoC00 C:1-86 Cytochrome c                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhh..................hhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: C:2-83 UniProt: 2-83                                                   --- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  1cno C  1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASNPAAA 86
                                    10        20        30        40        50        60        70        80      

Chain D from PDB  Type:PROTEIN  Length:86
 aligned with CY552_MARHY | P82903 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           CY552_MARHY    1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASLPADG 86
               SCOP domains d1cnod_ D: Cytochrome c552                                                             SCOP domains
               CATH domains 1cnoD00 D:1-86 Cytochrome c                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhh..................hhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: D:2-83 UniProt: 2-83                                                   --- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  1cno D  1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASNPAAA 86
                                    10        20        30        40        50        60        70        80      

Chain E from PDB  Type:PROTEIN  Length:86
 aligned with CY552_MARHY | P82903 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           CY552_MARHY    1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASLPADG 86
               SCOP domains d1cnoe_ E: Cytochrome c552                                                             SCOP domains
               CATH domains 1cnoE00 E:1-86 Cytochrome c                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhh..................hhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: E:2-83 UniProt: 2-83                                                   --- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  1cno E  1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASNPAAA 86
                                    10        20        30        40        50        60        70        80      

Chain F from PDB  Type:PROTEIN  Length:86
 aligned with CY552_MARHY | P82903 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           CY552_MARHY    1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASLPADG 86
               SCOP domains d1cnof_ F: Cytochrome c552                                                             SCOP domains
               CATH domains 1cnoF00 F:1-86 Cytochrome c                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhh..................hhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: F:2-83 UniProt: 2-83                                                   --- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  1cno F  1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASNPAAA 86
                                    10        20        30        40        50        60        70        80      

Chain G from PDB  Type:PROTEIN  Length:87
 aligned with CY552_MARHY | P82903 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
           CY552_MARHY    1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASLPADGQ 87
               SCOP domains d1cnog_ G: Cytochrome c552                                                              SCOP domains
               CATH domains 1cnoG00 G:1-87 Cytochrome c                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhh..................hhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: G:2-83 UniProt: 2-83                                                   ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1cno G  1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASNPAAAA 87
                                    10        20        30        40        50        60        70        80       

Chain H from PDB  Type:PROTEIN  Length:86
 aligned with CY552_MARHY | P82903 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           CY552_MARHY    1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASLPADG 86
               SCOP domains d1cnoh_ H: Cytochrome c552                                                             SCOP domains
               CATH domains 1cnoH00 H:1-86 Cytochrome c                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..................hhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: H:2-83 UniProt: 2-83                                                   --- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  1cno H  1 AGDIEAGKAKAAVCAACHGQNGISQVPIYPNLAGQKEQYLVAALKAYKAGQRQGGQAPVMQGQATALSDADIANLAAYYASNPAAA 86
                                    10        20        30        40        50        60        70        80      

   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, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (CY552_MARHY | P82903)
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: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.
biological process
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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

(no "Entries Sharing at Least One Protein Chain" available for 1CNO)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CNO)