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(-) Description

Title :  STRUCTURE OF QUINTUPLE MUTANT OF THE RAT OUTER MITOCONDRIAL CYTOCHROME B5.
 
Authors :  A. B. Cowley, A. Altuve, O. Kuchment, S. Terzyan, X. C. Zhang, M. Rivera, D. Benson
Date :  18 Apr 02  (Deposition) - 20 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  B (1x),C (1x)
Biol. Unit 6:  A  (1x)
Keywords :  Cytochrome, Heme, Protein Engineering, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. B. Cowley, A. Altuve, O. Kuchment, S. Terzyan, X. C. Zhang, M. Rivera, D. Benson
Toward Engineering The Stability And Hemin Binding Properties Of Microsomal Cytochromes B5 Into Rat Outer Mitochondrial Cytochrome B5: Examining The Influence Of Residues 25 And 71.
Biochemistry V. 41 11566 2002
PubMed-ID: 12269800  |  Reference-DOI: 10.1021/BI026005L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET11A
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentWATER SOLUBLE DOMAIN
    MutationYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x) BC 
Biological Unit 3 (1x)  CD
Biological Unit 4 (1x)   D
Biological Unit 5 (1x) B (1x)C (1x) 
Biological Unit 6 (1x)A   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:334 , HOH B:210 , HOH C:214 , HOH C:220 , HOH C:221 , HOH C:222BINDING SITE FOR RESIDUE MG A 301
2AC2SOFTWAREHOH A:333 , HOH A:364 , HOH C:213 , HOH C:216 , HOH D:318 , HOH D:319BINDING SITE FOR RESIDUE MG D 303
3AC3SOFTWAREHOH A:335 , HOH A:346 , HOH A:347 , HOH A:357 , HOH A:358 , HOH A:359BINDING SITE FOR RESIDUE MG A 304
4AC4SOFTWAREGLY A:-1 , SER A:0 , ASP A:1 , PRO A:2 , MET A:23 , LEU A:32 , PHE A:35 , HIS A:39 , PRO A:40 , VAL A:45 , LEU A:46 , GLN A:49 , PHE A:58 , VAL A:61 , HIS A:63 , SER A:64 , ALA A:67 , SER A:71 , HOH A:320BINDING SITE FOR RESIDUE HEM A 201
5AC5SOFTWAREMET B:23 , LEU B:32 , PHE B:35 , HIS B:39 , PRO B:40 , GLY B:41 , VAL B:45 , LEU B:46 , GLN B:49 , ALA B:54 , PHE B:58 , VAL B:61 , HIS B:63 , SER B:64 , ALA B:67 , SER C:57 , ASP C:60BINDING SITE FOR RESIDUE HEM B 201
6AC6SOFTWAREPRO B:40 , GLY B:42 , GLU B:43 , GLU B:44 , MET C:23 , LEU C:32 , PHE C:35 , HIS C:39 , PRO C:40 , GLY C:41 , VAL C:45 , LEU C:46 , GLN C:49 , ALA C:54 , SER C:57 , PHE C:58 , HIS C:63 , SER C:64 , ALA C:67 , SER C:71 , HOH C:202 , HOH C:217 , HOH C:224BINDING SITE FOR RESIDUE HEM C 201
7AC7SOFTWARELEU D:32 , PHE D:35 , HIS D:39 , PRO D:40 , GLY D:41 , VAL D:45 , LEU D:46 , ALA D:54 , PHE D:58 , VAL D:61 , HIS D:63 , SER D:64 , ALA D:67 , SER D:71BINDING SITE FOR RESIDUE HEM D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LJ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LJ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LJ0)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5B_RAT20-96
 
 
 
  4A:4-80
B:4-80
C:4-80
D:4-80
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5B_RAT51-58
 
 
 
  4A:35-42
B:35-42
C:35-42
D:35-42
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5B_RAT20-96
 
 
 
  2A:4-80
B:4-80
-
-
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5B_RAT51-58
 
 
 
  2A:35-42
B:35-42
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5B_RAT20-96
 
 
 
  2-
B:4-80
C:4-80
-
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5B_RAT51-58
 
 
 
  2-
B:35-42
C:35-42
-
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5B_RAT20-96
 
 
 
  2-
-
C:4-80
D:4-80
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5B_RAT51-58
 
 
 
  2-
-
C:35-42
D:35-42
Biological Unit 4 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5B_RAT20-96
 
 
 
  1-
-
-
D:4-80
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5B_RAT51-58
 
 
 
  1-
-
-
D:35-42
Biological Unit 5 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5B_RAT20-96
 
 
 
  2-
B:4-80
C:4-80
-
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5B_RAT51-58
 
 
 
  2-
B:35-42
C:35-42
-
Biological Unit 6 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5B_RAT20-96
 
 
 
  1A:4-80
-
-
-
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5B_RAT51-58
 
 
 
  1A:35-42
-
-
-

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000150061ENSRNOE00000104782chr19:37016959-37017126168CYB5B_RAT1-54544A:-1-38
B:-1-38
C:-1-38
D:2-38
40
40
40
37
1.2ENSRNOT000000150062ENSRNOE00000105131chr19:37036324-37036452129CYB5B_RAT55-97434A:39-81
B:39-81
C:39-81
D:39-81
43
43
43
43
1.3ENSRNOT000000150063ENSRNOE00000105523chr19:37036904-3703693330CYB5B_RAT98-107104A:82-87
B:82-87
C:82-86
D:82-87
6
6
5
6
1.4ENSRNOT000000150064ENSRNOE00000105590chr19:37045457-3704548529CYB5B_RAT108-117100--
1.5ENSRNOT000000150065ENSRNOE00000295386chr19:37048353-370507182366CYB5B_RAT117-146300--

(-) 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:89
 aligned with CYB5B_RAT | P04166 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:89
                                    24        34        44        54        64        74        84        94         
            CYB5B_RAT    15 GSDPAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKPK 103
               SCOP domains d1lj0a_ A: Cytochrome b5                                                                  SCOP domains
               CATH domains 1lj0A00 A:-1-87 Flavocytochrome B2, subunit A, domain 1                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eehhhhhh..ee..eeeeee..eeee...hhhhh...hhhhhhh....hhhhhhhhh.hhhhhhhhh..eeeee.hhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----CYTOCHROME_B5_2  PDB: A:4-80 UniProt: 20-96                                  ------- PROSITE (1)
                PROSITE (2) ------------------------------------CYTOCHRO--------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:-1-38 UniProt: 1-54    Exon 1.2  PDB: A:39-81 UniProt: 55-97      1.3    Transcript 1
                 1lj0 A  -1 GSDPAVTYYRLEEVAKRNTSEETWMVLHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMSKQYYIGDVHPNDLKPK  87
                                     8        18        28        38        48        58        68        78         

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with CYB5B_RAT | P04166 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:89
                                    24        34        44        54        64        74        84        94         
            CYB5B_RAT    15 GSDPAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKPK 103
               SCOP domains d1lj0b_ B: Cytochrome b5                                                                  SCOP domains
               CATH domains 1lj0B00 B:-1-87 Flavocytochrome B2, subunit A, domain 1                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eehhhhhhhhee..eeeeee..eeee...........hhhhhhh....hhhhhhhhh.hhhhhhhhh..eeeee.hhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----CYTOCHROME_B5_2  PDB: B:4-80 UniProt: 20-96                                  ------- PROSITE (1)
                PROSITE (2) ------------------------------------CYTOCHRO--------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:-1-38 UniProt: 1-54    Exon 1.2  PDB: B:39-81 UniProt: 55-97      1.3    Transcript 1
                 1lj0 B  -1 GSDPAVTYYRLEEVAKRNTSEETWMVLHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMSKQYYIGDVHPNDLKPK  87
                                     8        18        28        38        48        58        68        78         

Chain C from PDB  Type:PROTEIN  Length:88
 aligned with CYB5B_RAT | P04166 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:88
                                    24        34        44        54        64        74        84        94        
            CYB5B_RAT    15 GSDPAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKP 102
               SCOP domains d1lj0c_ C: Cytochrome b5                                                                 SCOP domains
               CATH domains 1lj0C00 C:-1-86 Flavocytochrome B2, subunit A, domain 1                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eehhhhhhhhee..eeeeee..eeee...hhhhh...hhhhhhh....hhhhhhhh..hhhhhhhhh..eeeee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----CYTOCHROME_B5_2  PDB: C:4-80 UniProt: 20-96                                  ------ PROSITE (1)
                PROSITE (2) ------------------------------------CYTOCHRO-------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: C:-1-38 UniProt: 1-54    Exon 1.2  PDB: C:39-81 UniProt: 55-97      1.3   Transcript 1
                 1lj0 C  -1 GSDPAVTYYRLEEVAKRNTSEETWMVLHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMSKQYYIGDVHPNDLKP  86
                                     8        18        28        38        48        58        68        78        

Chain D from PDB  Type:PROTEIN  Length:86
 aligned with CYB5B_RAT | P04166 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:86
                                    27        37        47        57        67        77        87        97      
            CYB5B_RAT    18 PAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKPK 103
               SCOP domains d1lj0d_ D: Cytochrome b5                                                               SCOP domains
               CATH domains 1lj0D00 D:2-87 Flavocytochrome B2, subunit A, domain 1                                 CATH domains
           Pfam domains (1) ----Cyt-b5-1lj0D01 D:6-80                                                      ------- Pfam domains (1)
           Pfam domains (2) ----Cyt-b5-1lj0D02 D:6-80                                                      ------- Pfam domains (2)
           Pfam domains (3) ----Cyt-b5-1lj0D03 D:6-80                                                      ------- Pfam domains (3)
           Pfam domains (4) ----Cyt-b5-1lj0D04 D:6-80                                                      ------- Pfam domains (4)
         Sec.struct. author ....eehhhhhhhhee..eeeeee..eeee...........hhhhhhhh...hhhhhhhhh.hhhhhhhhh..eeeee.hhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CYTOCHROME_B5_2  PDB: D:4-80 UniProt: 20-96                                  ------- PROSITE (1)
                PROSITE (2) ---------------------------------CYTOCHRO--------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: D:2-38 UniProt: 1-54  Exon 1.2  PDB: D:39-81 UniProt: 55-97      1.3    Transcript 1
                 1lj0 D   2 PAVTYYRLEEVAKRNTSEETWMVLHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMSKQYYIGDVHPNDLKPK  87
                                    11        21        31        41        51        61        71        81      

   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CYB5B_RAT | P04166)
molecular function
    GO:0045153    electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity    Enables the directed movement of electrons within the CoQH2-cytochrome c reductase complex.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    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.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
cellular component
    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.
    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:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYB5B_RAT | P041661awp 1b5m 1eue 1icc 2i89 3mus 4hil

(-) Related Entries Specified in the PDB File

1awp RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
1b5m RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
1cyo BOVINE CYTOCHROME B(5)
1eue RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
1icc RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5