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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CARNOSINE DIPEPTIDASE 1
 
Authors :  A. Dong, E. Dobrovetsky, A. Seitova, H. He, W. Tempel, I. Kozieradzki, C. H. Arrowsmith, J. Weigelt, C. Bountra, A. M. Edwards, A. Bochkarev, Structural Genomics Consortium (Sgc)
Date :  27 Jun 08  (Deposition) - 19 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Cndp1, Carnosine Dipeptidase 1, Structural Genomics, Structural Genomics Consortium, Sgc, Metallopeptidase M20 Family, Carboxypeptidase, Glycoprotein, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Dobrovetsky, A. Dong, A. Seitova, H. He, W. Tempel, I. Kozieradzki, C. H. Arrowsmith, J. Weigelt, C. Bountra, A. M. Edwards, A. Bochkarev, D. Cossar
Crystal Structure Of Human Carnosine Dipeptidase 1.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-ALA-HIS DIPEPTIDASE
    ChainsA, B
    EC Number3.4.13.20
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9 INSECT CELLS
    Expression System Taxid7108
    Expression System VectorPFHMSP-LIC-N
    Expression System Vector TypeBACULOVIRUS
    GeneCNDP1, CN1, CPGL2
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCARNOSINE DIPEPTIDASE 1, CNDP DIPEPTIDASE 1, SERUM CARNOSINASE, GLUTAMATE CARBOXYPEPTIDASE-LIKE PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2UNX15Ligand/IonUNKNOWN ATOM OR ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2UNX9Ligand/IonUNKNOWN ATOM OR ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
2UNX6Ligand/IonUNKNOWN ATOM OR ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 16)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2UNX15Ligand/IonUNKNOWN ATOM OR ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:139 , GLU A:174 , HIS A:452 , ZN A:2002 , UNX A:2004BINDING SITE FOR RESIDUE ZN A 2001
02AC2SOFTWAREHIS A:106 , ASP A:139 , GLU A:173 , ASP A:202 , ZN A:2001 , UNX A:2004BINDING SITE FOR RESIDUE ZN A 2002
03AC3SOFTWAREGLU A:173 , ASP A:202 , ZN A:2001 , ZN A:2002BINDING SITE FOR RESIDUE UNX A 2004
04AC4SOFTWAREHIS A:235 , THR A:337 , ARG B:350 , HIS B:452BINDING SITE FOR RESIDUE UNX A 2006
05AC5SOFTWAREASP A:331 , GLU A:332BINDING SITE FOR RESIDUE UNX A 2007
06AC6SOFTWAREVAL A:41 , ARG A:43BINDING SITE FOR RESIDUE UNX A 2008
07AC7SOFTWAREARG A:43BINDING SITE FOR RESIDUE UNX A 2009
08AC8SOFTWAREARG B:299BINDING SITE FOR RESIDUE UNX A 2010
09AC9SOFTWAREALA A:248 , ALA A:252 , HOH B:2040BINDING SITE FOR RESIDUE UNX A 2011
10BC1SOFTWARELEU A:243 , HIS A:244 , GLU A:245 , ALA A:248BINDING SITE FOR RESIDUE UNX A 2012
11BC2SOFTWAREARG A:299 , ARG B:230 , ASP B:231 , GLN B:232BINDING SITE FOR RESIDUE SO4 A 2003
12BC3SOFTWAREASP B:139 , GLU B:174 , HIS B:452 , ZN B:2002 , UNX B:2003BINDING SITE FOR RESIDUE ZN B 2001
13BC4SOFTWAREHIS B:106 , ASP B:139 , GLU B:173 , ASP B:202 , ZN B:2001 , UNX B:2003BINDING SITE FOR RESIDUE ZN B 2002
14BC5SOFTWAREHIS A:235 , ZN B:2001 , ZN B:2002BINDING SITE FOR RESIDUE UNX B 2003
15BC6SOFTWAREASP B:331 , GLU B:332 , HOH B:2027BINDING SITE FOR RESIDUE UNX B 2004
16BC7SOFTWAREPRO B:353 , PRO B:391BINDING SITE FOR RESIDUE UNX B 2005
17BC8SOFTWAREMET B:224 , VAL B:382 , SER B:384BINDING SITE FOR RESIDUE UNX B 2006
18BC9SOFTWAREPHE B:23 , THR B:26 , ASN B:149BINDING SITE FOR RESIDUE UNX B 2007
19CC1SOFTWARECYS B:229BINDING SITE FOR RESIDUE UNX B 2008

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:139 -Asn A:140
2Pro A:353 -His A:354
3Asp B:139 -Asn B:140
4Pro B:353 -His B:354

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027149I113VCNDP1_HUMANPolymorphism4263028A/BV87V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027149I113VCNDP1_HUMANPolymorphism4263028AV87V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027149I113VCNDP1_HUMANPolymorphism4263028BV87V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027149I113VCNDP1_HUMANPolymorphism4263028A/BV87V

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARGE_DAPE_CPG2_2PS00759 ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.CNDP1_HUMAN163-202
 
  2A:137-176
B:137-176
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARGE_DAPE_CPG2_2PS00759 ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.CNDP1_HUMAN163-202
 
  1A:137-176
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARGE_DAPE_CPG2_2PS00759 ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.CNDP1_HUMAN163-202
 
  1-
B:137-176
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARGE_DAPE_CPG2_2PS00759 ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.CNDP1_HUMAN163-202
 
  2A:137-176
B:137-176

(-) Exons   (0, 0)

(no "Exon" information available for 3DLJ)

(-) 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:471
 aligned with CNDP1_HUMAN | Q96KN2 from UniProtKB/Swiss-Prot  Length:507

    Alignment length:477
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       
          CNDP1_HUMAN    30 PPPALLEKVFQYIDLHQDEFVQTLKEWVAIESDSVQPVPRFRQELFRMMAVAADTLQRLGARVASVDMGPQQLPDGQSLPIPPIILAELGSDPTKGTVCFYGHLDVQPADRGDGWLTDPYVLTEVDGKLYGRGATDNKGPVLAWINAVSAFRALEQDLPVNIKFIIEGMEEAGSVALEELVEKEKDRFFSGVDYIVISDNLWISQRKPAITYGTRGNSYFMVEVKCRDQDFHSGTFGGILHEPMADLVALLGSLVDSSGHILVPGIYDEVVPLTEEEINTYKAIHLDLEEYRNSSRVEKFLFDTKEEILMHLWRYPSLSIHGIEGAFDEPGTKTVIPGRVIGKFSIRLVPHMNVSAVEKQVTRHLEDVFSKRNSSNKMVVSMTLGLHPWIANIDDTQYLAAKRAIRTVFGTEPDMIRDGSTIPIAKMFQEIVHKSVVLIPLGAVDDGEHSQNEKINRWNYIEGTKLFAAFFLEMAQL 506
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeeee...eee.--..eee...eeeeee.......eeeeeee......hhhhh........eee..eee......hhhhhhhhhhhhhhhhhh......eeeeeee.hhhhh..hhhhhhhhhh........eeee.......--..eeeeee.eeeeeeeeee.....ee.........hhhhhhhhhhh.....................hhhhhhhhhh...hhhhhhhhhh.......hhhhhhhhhhh..eeeeeeee..........ee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..ee....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh.--.ee...............eeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------ARGE_DAPE_CPG2_2  PDB: A:137-176        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dlj A   4 PPPALLEKVFQYIDLHQDEFVQTLKEWVAIESDSVQPVPRFRQELFRMMAVAADTLQRLGARVASVDMGPQQL--GQSLPIPPVILAELGSDPTKGTVCFYGHLDVQPADRGDGWLTDPYVLTEVDGKLYGRGATDNKGPVLAWINAVSAFRALEQDLPVNIKFIIEGMEEAGSVALEELVEKEKDRFFSGVDYIVISDNLWIS--KPAITYGTRGNSYFMVEVKCRDQDFHSGTFGGILHEPMADLVALLGSLVDSSGHILVPGIYDEVVPLTEEEINTYKAIHLDLEEYRNSSRVEKFLFDTKEEILMHLWRYPSLSIHGIEGAFDEPGTKTVIPGRVIGKFSIRLVPHMNVSAVEKQVTRHLEDVFSKRNSSNKMVVSMTLGLHPWIANIDDTQYLAAKRAIRTVFGTEPDMIRDGSTIPIAKMFQEIVH--VVLIPLGAVDDGEHSQNEKINRWNYIEGTKLFAAFFLEMAQL 480
                                    13        23        33        43        53        63        73  |  |  83        93       103       113       123       133       143       153       163       173       183       193       203   |  |213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433  |  | 443       453       463       473       
                                                                                                   76 79                                                                                                                             207  |                                                                                                                                                                                                                               436  |                                         
                                                                                                                                                                                                                                        210                                                                                                                                                                                                                                  439                                         

Chain B from PDB  Type:PROTEIN  Length:467
 aligned with CNDP1_HUMAN | Q96KN2 from UniProtKB/Swiss-Prot  Length:507

    Alignment length:473
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503   
          CNDP1_HUMAN    34 LLEKVFQYIDLHQDEFVQTLKEWVAIESDSVQPVPRFRQELFRMMAVAADTLQRLGARVASVDMGPQQLPDGQSLPIPPIILAELGSDPTKGTVCFYGHLDVQPADRGDGWLTDPYVLTEVDGKLYGRGATDNKGPVLAWINAVSAFRALEQDLPVNIKFIIEGMEEAGSVALEELVEKEKDRFFSGVDYIVISDNLWISQRKPAITYGTRGNSYFMVEVKCRDQDFHSGTFGGILHEPMADLVALLGSLVDSSGHILVPGIYDEVVPLTEEEINTYKAIHLDLEEYRNSSRVEKFLFDTKEEILMHLWRYPSLSIHGIEGAFDEPGTKTVIPGRVIGKFSIRLVPHMNVSAVEKQVTRHLEDVFSKRNSSNKMVVSMTLGLHPWIANIDDTQYLAAKRAIRTVFGTEPDMIRDGSTIPIAKMFQEIVHKSVVLIPLGAVDDGEHSQNEKINRWNYIEGTKLFAAFFLEMAQL 506
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeeee...ee..---..ee...eeeeee.......eeeeeee......hhhhh........eee..eee......hhhhhhhhhhhhhhhhhh......eeeeeee.hhhhh..hhhhhhhhh.........eeee.......--..eeeeee.eeeeeeeeee.....ee.........hhhhhhhhhhh.....................hhhhhhhhhh...hhhhhhhhhh.......hhhhhhhhhhh..eeeeeeee..........ee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..ee....hhhhhhhhhhhhhhh-...eeeee...hhhhhhhhhhhh..eee...............eeehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------ARGE_DAPE_CPG2_2  PDB: B:137-176        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dlj B   8 LLEKVFQYIDLHQDEFVQTLKEWVAIESDSVQPVPRFRQELFRMMAVAADTLQRLGARVASVDMGPQQL---QSLPIPPVILAELGSDPTKGTVCFYGHLDVQPADRGDGWLTDPYVLTEVDGKLYGRGATDNKGPVLAWINAVSAFRALEQDLPVNIKFIIEGMEEAGSVALEELVEKEKDRFFSGVDYIVISDNLWIS--KPAITYGTRGNSYFMVEVKCRDQDFHSGTFGGILHEPMADLVALLGSLVDSSGHILVPGIYDEVVPLTEEEINTYKAIHLDLEEYRNSSRVEKFLFDTKEEILMHLWRYPSLSIHGIEGAFDEPGTKTVIPGRVIGKFSIRLVPHMNVSAVEKQVTRHLEDVFSKRNSSNKMVVSMTLGLHPWIANIDDTQYLAAKRAIRTVF-TEPDMIRDGSTIPIAKMFQEIVHKSVVLIPLGAVDDGEHSQNEKINRWNYIEGTKLFAAFFLEMAQL 480
                                    17        27        37        47        57        67        |-  |     87        97       107       117       127       137       147       157       167       177       187       197       207  |    217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407    | |417       427       437       447       457       467       477   
                                                                                               76  80                                                                                                                            207  |                                                                                                                                                                                                       412 |                                                                  
                                                                                                                                                                                                                                    210                                                                                                                                                                                                         414                                                                  

   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  (0, 0)

(no "SCOP Domain" information available for 3DLJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CNDP1_HUMAN | Q96KN2)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0034701    tripeptidase activity    Catalysis of the hydrolysis of a tripeptide.
biological process
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0032268    regulation of cellular protein metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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