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(-) Description

Title :  CRYSTAL STRUCTURE OF WATER-SOLUBLE CHLOROPHYLL PROTEIN FROM LEPIDIUM VIRGINICUM AT 2.00 ANGSTROM RESOLUTION
 
Authors :  D. Horigome, H. Satoh, N. Itoh, K. Mitsunaga, I. Oonishi, A. Nakagawa, A. Uchida
Date :  08 Jun 06  (Deposition) - 26 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Trefoil, Tetramer, Plant, Lepidium Virginicum, Chlorophyll, Water-Soluble Chlorophyll Protein, Singlet Oxygen, Photooxidation, Chlorophyll Carrier, Kunitz (Sti) Inhibitors, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Horigome, H. Satoh, N. Itoh, K. Mitsunaga, I. Oonishi, A. Nakagawa, A. Uchida
Structural Mechanism And Photoprotective Function Of Water-Soluble Chlorophyll-Binding Protein.
J. Biol. Chem. V. 282 6525 2007
PubMed-ID: 17170107  |  Reference-DOI: 10.1074/JBC.M609458200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - WATER-SOLUBLE CHLOROPHYLL PROTEIN
    Chains: A, B, C, D
    Fragment: RESIDUES 1-180
    Organism Scientific: LEPIDIUM VIRGINICUM
    Organism Taxid: 59292
    Tissue: LEAF

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CLA4Ligand/IonCHLOROPHYLL A

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:35 , PRO A:36 , ALA A:37 , ASN A:38 , LEU A:47 , THR A:52 , SER A:53 , LEU A:54 , GLN A:57 , ILE A:89 , TRP A:90 , LEU A:91 , TRP A:154 , GLN B:57 , ILE B:89 , CLA B:1001 , HOH B:1023 , LEU C:44 , LEU D:44 , CLA D:1001BINDING SITE FOR RESIDUE CLA A 1001
2AC2SOFTWARELEU A:44 , LEU A:54 , GLN A:57 , ILE A:89 , CLA A:1001 , HOH A:1030 , VAL B:35 , PRO B:36 , ALA B:37 , ASN B:38 , LEU B:47 , THR B:52 , SER B:53 , LEU B:54 , GLN B:57 , ILE B:89 , LEU B:91 , TRP B:154 , LEU C:44 , CLA C:1001 , LEU D:41 , LEU D:44 , LEU D:153 , TRP D:154 , CLA D:1001BINDING SITE FOR RESIDUE CLA B 1001
3AC3SOFTWAREASP A:40 , LEU A:41 , HIS A:43 , LEU A:44 , LEU B:44 , CLA B:1001 , VAL C:35 , PRO C:36 , ASN C:38 , LEU C:47 , THR C:52 , SER C:53 , LEU C:54 , GLN C:57 , LEU C:60 , ILE C:89 , TRP C:90 , LEU C:91 , TRP C:154 , GLN D:57 , ILE D:89 , CLA D:1001 , HOH D:1020BINDING SITE FOR RESIDUE CLA C 1001
4AC4SOFTWARELEU A:44 , CLA A:1001 , ASN B:38 , LEU B:41 , TRP B:154 , CLA B:1001 , GLN C:57 , ILE C:89 , CLA C:1001 , HOH C:1034 , VAL D:35 , PRO D:36 , ALA D:37 , ASN D:38 , LEU D:47 , THR D:52 , SER D:53 , LEU D:54 , ILE D:89 , TRP D:90 , LEU D:91 , TRP D:154BINDING SITE FOR RESIDUE CLA D 1001

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:92
2B:45 -B:92
3C:45 -C:92
4D:45 -D:92

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Cys A:45 -Pro A:46
2Cys B:45 -Pro B:46
3Cys C:45 -Pro C:46
4Cys D:45 -Pro D:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DRE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DRE)

(-) Exons   (0, 0)

(no "Exon" information available for 2DRE)

(-) Sequences/Alignments

Asymmetric/Biological 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:172
 aligned with O04797_LEPVR | O04797 from UniProtKB/TrEMBL  Length:223

    Alignment length:178
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197        
         O04797_LEPVR    28 NDEEPVKDTNGNPLKIETRYFIQPASDNNGGGLVPANVDLSHLCPLGIVRTSLPYQPGLPVTISTPSSSEGNDVLTNTNIAITFDAPIWLCPSSKTWTVDSSSEEKYIITGGDPKSGESFFRIEKYGNGKNTYKLVRYDNGEGKSVGSTKSLWGPALVLNDDDDSDENAFPIKFREVD 205
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee........eeee..........eeee..........eeee................eeee.............ee........ee......hhhhh.eeee.......eeeeee....eeeeeeee....eeeee..------....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dre A   2 NDEEPVKDTNGNPLKIETRYFIQPASDNNGGGLVPANVDLSHLCPLGIVRTSLPYQPGLPVTISTPSSSEGNDVLTNTNIAITFDAPIWLCPSSKTWTVDSSSEEKYIITGGDPKSGESFFRIEKYGNGKNTYKLVRYDNGEGKSVGSTKSLWGPALVLND------NAFPIKFREVD 179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161|      171        
                                                                                                                                                                                          162    169          


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with O04797_LEPVR | O04797 from UniProtKB/TrEMBL  Length:223

    Alignment length:176
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199      
         O04797_LEPVR    30 EEPVKDTNGNPLKIETRYFIQPASDNNGGGLVPANVDLSHLCPLGIVRTSLPYQPGLPVTISTPSSSEGNDVLTNTNIAITFDAPIWLCPSSKTWTVDSSSEEKYIITGGDPKSGESFFRIEKYGNGKNTYKLVRYDNGEGKSVGSTKSLWGPALVLNDDDDSDENAFPIKFREVD 205
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee........eeee..........eeee.........eeeee................eeee.............ee........ee......hhhhh.eeee.......eeee.---.....eeeee....eeeee............eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dre B   4 EEPVKDTNGNPLKIETRYFIQPASDNNGGGLVPANVDLSHLCPLGIVRTSLPYQPGLPVTISTPSSSEGNDVLTNTNIAITFDAPIWLCPSSKTWTVDSSSEEKYIITGGDPKSGESFFRIEKYGNGKNTYKLVR---GEGKSVGSTKSLWGPALVLNDDDDSDENAFPIKFREVD 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    |  143       153       163       173      
                                                                                                                                                                138 142                                     


Chain C from PDB  Type:PROTEIN  Length:177
 aligned with O04797_LEPVR | O04797 from UniProtKB/TrEMBL  Length:223

    Alignment length:177
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       
         O04797_LEPVR    29 DEEPVKDTNGNPLKIETRYFIQPASDNNGGGLVPANVDLSHLCPLGIVRTSLPYQPGLPVTISTPSSSEGNDVLTNTNIAITFDAPIWLCPSSKTWTVDSSSEEKYIITGGDPKSGESFFRIEKYGNGKNTYKLVRYDNGEGKSVGSTKSLWGPALVLNDDDDSDENAFPIKFREVD 205
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee........eeee..........eeee..........eeee..............eeeeee.............ee........ee..........eeeeee.......eeeeee....eeeeeeeee..eeeeee............eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dre C   3 DEEPVKDTNGNPLKIETRYFIQPASDNNGGGLVPANVDLSHLCPLGIVRTSLPYQPGLPVTISTPSSSEGNDVLTNTNIAITFDAPIWLCPSSKTWTVDSSSEEKYIITGGDPKSGESFFRIEKYGNGKNTYKLVRYDNGEGKSVGSTKSLWGPALVLNDDDDSDENAFPIKFREVD 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       


Chain D from PDB  Type:PROTEIN  Length:177
 aligned with O04797_LEPVR | O04797 from UniProtKB/TrEMBL  Length:223

    Alignment length:177
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       
         O04797_LEPVR    29 DEEPVKDTNGNPLKIETRYFIQPASDNNGGGLVPANVDLSHLCPLGIVRTSLPYQPGLPVTISTPSSSEGNDVLTNTNIAITFDAPIWLCPSSKTWTVDSSSEEKYIITGGDPKSGESFFRIEKYGNGKNTYKLVRYDNGEGKSVGSTKSLWGPALVLNDDDDSDENAFPIKFREVD 205
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee........eeee..........eeee..........eeee................eeee...........eeee........eeeee...hhhhh.eeee.......eeeeee....eeeeeeeee..eeeeee.....hhhhh..eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dre D   3 DEEPVKDTNGNPLKIETRYFIQPASDNNGGGLVPANVDLSHLCPLGIVRTSLPYQPGLPVTISTPSSSEGNDVLTNTNIAITFDAPIWLCPSSKTWTVDSSSEEKYIITGGDPKSGESFFRIEKYGNGKNTYKLVRYDNGEGKSVGSTKSLWGPALVLNDDDDSDENAFPIKFREVD 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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 2DRE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DRE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DRE)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (O04797_LEPVR | O04797)
molecular function
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.

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