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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PHOSPHOPANTOTHENOYLCYSTEINE DECARBOXYLASE
 
Authors :  N. Manoj, S. E. Ealick
Date :  17 Sep 03  (Deposition) - 23 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (3x)
Biol. Unit 5:  C  (3x)
Keywords :  Alpha-Beta Sandwich, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Manoj, S. E. Ealick
Unusual Space-Group Pseudosymmetry In Crystals Of Human Phosphopantothenoylcysteine Decarboxylase.
Acta Crystallogr. , Sect. D V. 59 1762 2003
PubMed-ID: 14501115  |  Reference-DOI: 10.1107/S0907444903016214

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN MDS018
    ChainsA, B, C, D
    EC Number4.1.1.36
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEX-HTA
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCOAC
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1FMN3Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1FMN3Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1FMN3Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 5 (1, 3)
No.NameCountTypeFull Name
1FMN3Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:25 , GLY A:26 , SER A:27 , VAL A:28 , THR A:53 , PHE A:59 , GLU A:75 , TRP A:76 , TRP A:79 , ASP A:104 , ALA A:105 , ASN A:106 , THR A:107 , CYS A:116 , ALA A:138 , MET A:139 , MET A:143BINDING SITE FOR RESIDUE FMN A 801
2AC2SOFTWARETHR B:25 , GLY B:26 , SER B:27 , VAL B:28 , THR B:53 , GLU B:75 , TRP B:76 , TRP B:79 , ASP B:104 , ALA B:105 , ASN B:106 , THR B:107 , CYS B:116 , ALA B:138 , MET B:139 , MET B:143BINDING SITE FOR RESIDUE FMN B 802
3AC3SOFTWAREGLY C:26 , SER C:27 , VAL C:28 , THR C:53 , GLU C:75 , TRP C:76 , TRP C:79 , HIS C:88 , ASP C:104 , ALA C:105 , ASN C:106 , THR C:107 , CYS C:116 , ASP C:117 , ALA C:138 , MET C:139 , MET C:143BINDING SITE FOR RESIDUE FMN C 803
4AC4SOFTWARETHR D:25 , GLY D:26 , SER D:27 , VAL D:28 , THR D:53 , GLU D:75 , TRP D:76 , TRP D:79 , ASP D:104 , ALA D:105 , ASN D:106 , THR D:107 , CYS D:116 , ALA D:138 , MET D:139 , MET D:143BINDING SITE FOR RESIDUE FMN D 804

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:116 -A:122
2B:116 -B:122
3C:116 -C:122
4D:116 -D:122

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:101 -Pro A:102
2Ala B:101 -Pro B:102
3Ala C:101 -Pro C:102
4Ala D:101 -Pro D:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

Asymmetric Unit (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068974I78MCOAC_HUMANPolymorphism2304899A/B/C/DM78M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068974I78MCOAC_HUMANPolymorphism2304899AM78M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068974I78MCOAC_HUMANPolymorphism2304899BM78M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068974I78MCOAC_HUMANPolymorphism2304899CM78M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068974I78MCOAC_HUMANPolymorphism2304899DM78M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 5 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068974I78MCOAC_HUMANPolymorphism2304899CM78M

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QZU)

(-) Exons   (5, 20)

Asymmetric Unit (5, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003429321ENSE00001242936chr15:75315896-7531596772COAC_HUMAN-00--
1.2ENST000003429322ENSE00001045767chr15:75320588-75320794207COAC_HUMAN1-45454A:14-45 (gaps)
B:16-45 (gaps)
C:14-45 (gaps)
D:16-45 (gaps)
32
30
32
30
1.3ENST000003429323ENSE00001045762chr15:75335782-7533587796COAC_HUMAN46-77324A:46-77
B:46-77
C:46-77
D:46-77
32
32
32
32
1.4ENST000003429324ENSE00000885757chr15:75336727-75336855129COAC_HUMAN78-120434A:78-120
B:78-120
C:78-120
D:78-120
43
43
43
43
1.5ENST000003429325ENSE00000575433chr15:75340894-75341062169COAC_HUMAN121-177574A:121-165
B:121-165
C:121-165
D:121-165
45
45
45
45
1.6ENST000003429326ENSE00001381226chr15:75341491-753430671577COAC_HUMAN177-204284A:184-194
B:184-191
C:184-194
D:184-191
11
8
11
8

(-) 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:160
 aligned with COAC_HUMAN | Q96CD2 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:181
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193 
           COAC_HUMAN    14 MERKFHVLVGVTGSVAALKLPLLVSKLLDIPGLEVAVVTTERAKHFYSPQDIPVTLYSDADEWEIWKSRSDPVLHIDLRRWADLLLVAPLDANTLGKVASGICDNLLTCVMRAWDRSKPLLFCPAMNTAMWEHPITAQQVDQLKAFGYVEIPCVAKKLVCGDEGLGAMAEVGTIVDKVKEV 194
               SCOP domains d1qzua_ A: 4'-phosphopantoth   enoylcysteine decarboxylase (PPC decarboxylase, halotolerance protein Hal3a)                                                                           SCOP domains
               CATH domains 1qzuA00 A:14-194  [code=3.40   .50.1950, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhhhh---.eeeeeee.hhhhhh.hhhhh...eehhhhhhhh.......hhhhhhhh...eeeeeeehhhhhhhhhh....hhhhhhhhh........eee..hhhhhh..hhhhhhhhhhh.......------------------.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------M-------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:14-45 (gaps)   Exon 1.3  PDB: A:46-77          Exon 1.4  PDB: A:78-120 UniProt: 78-120    Exon 1.5  PDB: A:121-165 UniProt: 121-177 [INCOMPLETE]   ----------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6           Transcript 1 (2)
                 1qzu A  14 MERKFHVLVGVTGSVAALKLPLLVSKLL---GLEVAVVTTERAKHFYSPQDIPVTLYSDADEWEMWKSRSDPVLHIDLRRWADLLLVAPLDANTLGKVASGICDNLLTCVMRAWDRSKPLLFCPAMNTAMWEHPITAQQVDQLKAFGYVEIP------------------VGTIVDKVKEV 194
                                    23        33       | - |      53        63        73        83        93       103       113       123       133       143       153       163 |       -         -|      193 
                                                      41  45                                                                                                                     165                184          

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with COAC_HUMAN | Q96CD2 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:176
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185      
           COAC_HUMAN    16 RKFHVLVGVTGSVAALKLPLLVSKLLDIPGLEVAVVTTERAKHFYSPQDIPVTLYSDADEWEIWKSRSDPVLHIDLRRWADLLLVAPLDANTLGKVASGICDNLLTCVMRAWDRSKPLLFCPAMNTAMWEHPITAQQVDQLKAFGYVEIPCVAKKLVCGDEGLGAMAEVGTIVDKV 191
               SCOP domains d1qzub_ B: 4'-phosphopanto   thenoylcysteine decarboxylase (PPC decarboxylase, halotolerance protein Hal3a)                                                                      SCOP domains
               CATH domains 1qzuB00 B:16-191  [code=3.   40.50.1950, no name defined]                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhhh---..eeeeee.hhhhhh.hhhhh...eehhhhhhhh.......hhhhhhhh...eeeeeeehhhhhhhhhh....hhhhhhhhh........eee..hhhhhh..hhhhhhhhhhh.......------------------.hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------M----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:16-45 (gaps) Exon 1.3  PDB: B:46-77          Exon 1.4  PDB: B:78-120 UniProt: 78-120    Exon 1.5  PDB: B:121-165 UniProt: 121-177 [INCOMPLETE]   -------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6        Transcript 1 (2)
                 1qzu B  16 RKFHVLVGVTGSVAALKLPLLVSKLL---GLEVAVVTTERAKHFYSPQDIPVTLYSDADEWEMWKSRSDPVLHIDLRRWADLLLVAPLDANTLGKVASGICDNLLTCVMRAWDRSKPLLFCPAMNTAMWEHPITAQQVDQLKAFGYVEIP------------------VGTIVDKV 191
                                    25        35     |  45        55        65        75        85        95       105       115       125       135       145       155       165         -       185      
                                                    41  45                                                                                                                     165                184       

Chain C from PDB  Type:PROTEIN  Length:160
 aligned with COAC_HUMAN | Q96CD2 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:181
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193 
           COAC_HUMAN    14 MERKFHVLVGVTGSVAALKLPLLVSKLLDIPGLEVAVVTTERAKHFYSPQDIPVTLYSDADEWEIWKSRSDPVLHIDLRRWADLLLVAPLDANTLGKVASGICDNLLTCVMRAWDRSKPLLFCPAMNTAMWEHPITAQQVDQLKAFGYVEIPCVAKKLVCGDEGLGAMAEVGTIVDKVKEV 194
               SCOP domains d1qzuc_ C: 4'-phosphopantoth   enoylcysteine decarboxylase (PPC decarboxylase, halotolerance protein Hal3a)                                                                           SCOP domains
               CATH domains 1qzuC00 C:14-194  [code=3.40   .50.1950, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhhhh---.eeeeeee.hhhhhh.hhhhh...eehhhhhhhh.......hhhhhhhh...eeeeeeehhhhhhhhhh....hhhhhhhhh........eee..hhhhhh..hhhhhhhhhhh.......------------------.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------M-------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: C:14-45 (gaps)   Exon 1.3  PDB: C:46-77          Exon 1.4  PDB: C:78-120 UniProt: 78-120    Exon 1.5  PDB: C:121-165 UniProt: 121-177 [INCOMPLETE]   ----------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6           Transcript 1 (2)
                 1qzu C  14 MERKFHVLVGVTGSVAALKLPLLVSKLL---GLEVAVVTTERAKHFYSPQDIPVTLYSDADEWEMWKSRSDPVLHIDLRRWADLLLVAPLDANTLGKVASGICDNLLTCVMRAWDRSKPLLFCPAMNTAMWEHPITAQQVDQLKAFGYVEIP------------------VGTIVDKVKEV 194
                                    23        33       | - |      53        63        73        83        93       103       113       123       133       143       153       163 |       -         -|      193 
                                                      41  45                                                                                                                     165                184          

Chain D from PDB  Type:PROTEIN  Length:155
 aligned with COAC_HUMAN | Q96CD2 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:176
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185      
           COAC_HUMAN    16 RKFHVLVGVTGSVAALKLPLLVSKLLDIPGLEVAVVTTERAKHFYSPQDIPVTLYSDADEWEIWKSRSDPVLHIDLRRWADLLLVAPLDANTLGKVASGICDNLLTCVMRAWDRSKPLLFCPAMNTAMWEHPITAQQVDQLKAFGYVEIPCVAKKLVCGDEGLGAMAEVGTIVDKV 191
               SCOP domains d1qzud_ D: 4'-phosphopanto   thenoylcysteine decarboxylase (PPC decarboxylase, halotolerance protein Hal3a)                                                                      SCOP domains
               CATH domains 1qzuD00 D:16-191  [code=3.   40.50.1950, no name defined]                                                                                                                        CATH domains
           Pfam domains (1) --Flavoprotein-1qzuD01 D:1   8-149                                                                                                    ----------------                  -------- Pfam domains (1)
           Pfam domains (2) --Flavoprotein-1qzuD02 D:1   8-149                                                                                                    ----------------                  -------- Pfam domains (2)
           Pfam domains (3) --Flavoprotein-1qzuD03 D:1   8-149                                                                                                    ----------------                  -------- Pfam domains (3)
           Pfam domains (4) --Flavoprotein-1qzuD04 D:1   8-149                                                                                                    ----------------                  -------- Pfam domains (4)
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhhh---.eeeeeee.hhhhhh.hhhhh...eehhhhhhhh.......hhhhhhhh...eeeeeeehhhhhhhhhh....hhhhhhhhh........eee..hhhhhh..hhhhhhhhhhh.......------------------.hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------M----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: D:16-45 (gaps) Exon 1.3  PDB: D:46-77          Exon 1.4  PDB: D:78-120 UniProt: 78-120    Exon 1.5  PDB: D:121-165 UniProt: 121-177 [INCOMPLETE]   -------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6        Transcript 1 (2)
                 1qzu D  16 RKFHVLVGVTGSVAALKLPLLVSKLL---GLEVAVVTTERAKHFYSPQDIPVTLYSDADEWEMWKSRSDPVLHIDLRRWADLLLVAPLDANTLGKVASGICDNLLTCVMRAWDRSKPLLFCPAMNTAMWEHPITAQQVDQLKAFGYVEIP------------------VGTIVDKV 191
                                    25        35     |  45        55        65        75        85        95       105       115       125       135       145       155       165         -       185      
                                                    41  45                                                                                                                     165                184       

   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  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (COAC_HUMAN | Q96CD2)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004633    phosphopantothenoylcysteine decarboxylase activity    Catalysis of the reaction: N-[(R)-4-phosphonatopantothenoyl]-L-cysteinate + H(+) = CO(2) + pantetheine 4'-phosphate.
    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).
biological process
    GO:0015937    coenzyme A biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
    GO:0009108    coenzyme biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzymes, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
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.

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