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(-) Description

Title :  CRYSTAL STRUCTURE OF PSYCHROPHILIC SUBTILISIN-LIKE SERINE PROTEASE APA1 FROM ANTARCTIC PSYCHROTROPH PSEUDOALEROMONAS SP. AS-11, COMPLEXED WITH INHIBITOR CHYMOSTATIN
 
Authors :  D. Dong, K. Watanabe
Date :  16 Dec 04  (Deposition) - 21 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  B,D  (1x)
Biol. Unit 4:  A,C  (1x)
Keywords :  Subtilisin-Like Alpha/Beta Domain, Insert Beta Barrel Domain, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Dong, K. Watanabe
Crystal Structure Of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 At 0. 16 Nm Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALKALINE SERINE PROTEASE
    Chains: A, B
    EC Number: 3.4.21.-
    Fragment: RESIDUES 1-441
    Organism Scientific: PSEUDOALTEROMONAS SP.
    Organism Taxid: 247492
    Other Details: EXTRACELLULAR ENZYME
    Strain: AS-11
    Synonym: SUBTILISIN-LIKE PROTEASE
 
Molecule 2 - CHYMOSTATIN
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CSI2Mod. Amino AcidAMINO-(2-IMINO-HEXAHYDRO-PYRIMIDIN-4-YL)-ACETIC ACID
3MG8Ligand/IonMAGNESIUM ION
4PHA2Mod. Amino AcidPHENYLALANINAL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CSI2Mod. Amino AcidAMINO-(2-IMINO-HEXAHYDRO-PYRIMIDIN-4-YL)-ACETIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4PHA2Mod. Amino AcidPHENYLALANINAL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CSI-1Mod. Amino AcidAMINO-(2-IMINO-HEXAHYDRO-PYRIMIDIN-4-YL)-ACETIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4PHA-1Mod. Amino AcidPHENYLALANINAL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CSI1Mod. Amino AcidAMINO-(2-IMINO-HEXAHYDRO-PYRIMIDIN-4-YL)-ACETIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4PHA1Mod. Amino AcidPHENYLALANINAL
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CSI1Mod. Amino AcidAMINO-(2-IMINO-HEXAHYDRO-PYRIMIDIN-4-YL)-ACETIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4PHA1Mod. Amino AcidPHENYLALANINAL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:2 , ASP A:39 , ILE A:76 , ASN A:78 , GLU A:80 , VAL A:82BINDING SITE FOR RESIDUE CA A 603
02AC2SOFTWAREASP A:404 , LEU A:405 , VAL A:407 , GLY A:409 , ASP A:411 , MG A:607BINDING SITE FOR RESIDUE CA A 604
03AC3SOFTWAREGLU B:2 , ASP B:39 , ILE B:76 , ASN B:78 , GLU B:80 , VAL B:82BINDING SITE FOR RESIDUE CA B 605
04AC4SOFTWAREASP B:404 , LEU B:405 , VAL B:407 , GLY B:409 , ASP B:411 , MG B:610BINDING SITE FOR RESIDUE CA B 606
05AC5SOFTWAREASP A:404 , LEU A:405 , ASP A:411 , THR A:414 , GLY A:415 , TYR A:416 , GLY A:417 , CA A:604BINDING SITE FOR RESIDUE MG A 607
06AC6SOFTWAREALA A:169 , TYR A:171 , VAL A:174 , GLN A:195 , MG A:609BINDING SITE FOR RESIDUE MG A 608
07AC7SOFTWAREVAL A:174 , SER A:176 , GLN A:195 , GLU A:197 , MG A:608BINDING SITE FOR RESIDUE MG A 609
08AC8SOFTWAREASP B:404 , LEU B:405 , ASP B:411 , THR B:414 , GLY B:415 , TYR B:416 , GLY B:417 , CA B:606BINDING SITE FOR RESIDUE MG B 610
09AC9SOFTWAREALA B:169 , TYR B:171 , VAL B:174 , GLN B:195 , MG B:612BINDING SITE FOR RESIDUE MG B 611
10BC1SOFTWAREVAL B:174 , SER B:176 , GLN B:195 , GLU B:197 , MG B:611BINDING SITE FOR RESIDUE MG B 612
11BC2SOFTWAREHOH B:772 , HOH B:780 , HOH B:786 , HOH B:798 , HOH B:807 , HOH B:839BINDING SITE FOR RESIDUE MG B 613
12BC3SOFTWAREHOH B:676 , HOH B:728BINDING SITE FOR RESIDUE MG B 614
13BC4SOFTWAREASP A:30 , HIS A:65 , PHE A:99 , TRP A:104 , LEU A:110 , SER A:129 , LEU A:130 , GLY A:131 , GLY A:132 , GLY A:158 , ASN A:159 , SER A:166 , GLY A:367 , THR A:368 , SER A:369 , HOH A:724 , HOH C:686 , HOH C:717 , HOH C:731 , HOH C:832 , HOH C:833BINDING SITE FOR CHAIN C OF CHYMOSTATIN
14BC5SOFTWAREASP B:30 , HIS B:65 , PHE B:99 , TRP B:104 , LEU B:110 , SER B:129 , LEU B:130 , GLY B:131 , GLY B:132 , GLY B:158 , ASN B:159 , SER B:166 , TYR B:167 , GLY B:367 , THR B:368 , SER B:369 , HOH D:794 , HOH D:797 , HOH D:814BINDING SITE FOR CHAIN D OF CHYMOSTATIN

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:27 -A:117
2A:260 -A:269
3A:277 -A:298
4A:389 -A:432
5B:27 -B:117
6B:260 -B:269
7B:277 -B:298
8B:389 -B:432

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:167 -Pro A:168
2Tyr B:167 -Pro B:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WVM)

(-) 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:435
 aligned with Q65Z69_9GAMM | Q65Z69 from UniProtKB/TrEMBL  Length:817

    Alignment length:435
                                   154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574     
         Q65Z69_9GAMM   145 AETTPWGQTFVGATVLSDSQAGNRTICIIDSGYDRSHNDLNANNVTGTNNSGTGNWYQPGNNNAHGTHVAGTIAAIANNEGVVGVMPNQNANIHIVKVFNEAGWGYSSSLVAAIDTCVNSGGANVVTMSLGGSGSTTTERNALNTHYNNGVLLIAAAGNAGDSSYSYPASYDSVMSVAAVDSNLDHAAFSQYTDQVEISGPGEAILSTVTVGEGRLADITIGGQSYFSNGVVPHNRLTPSGTSYAPAPINASATGALAECTVNGTSFSCGNMANKICLVERVGNQGSSYPEINSTKACKTAGAKGIIVYSNSALPGLQNPFLVDANSDITVPSVSVDRATGLALKAKLGQSTTVSNQGNQDYEYYNGTSMATPHVSGVATLVWSYHPECSASQVRAALNATADDLSVAGRDNQTGYGMINAVAAKAYLDESCTGP 579
               SCOP domains d1wvma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1wvmA01 A:1-214,A:360-435  [code=3.40.50.200, no name defined]                                                                                                                                                        1wvmA02 A:215-359  [code=3.50.30.30, no name defined]                                                                                            1wvmA01 A:1-214,A:360-435  [code=3.40.50.200, no name defined]               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh...hhhh.eeeeee.............eeee................hhhhhhhhhhhh................eeeeee.ee..ee....hhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhh..eeeee.................eeeeeee...............eeeeee...eeee.....eeeeeeee..ee.hhhh.ee.eeeee....eee.....eeeeeeeeeeee..eee......eeeeee.........hhhhhhhhhhhh...eeeee...........eee.........eeeehhhhhhhhhh....eeeeeeeeee.eeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.................hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wvm A   1 AETTPWGQTFVGATVLSDSQAGNRTICIIDSGYDRSHNDLNANNVTGTNNSGTGNWYQPGNNNAHGTHVAGTIAAIANNEGVVGVMPNQNANIHIVKVFNEAGWGYSSSLVAAIDTCVNSGGANVVTMSLGGSGSTTTERNALNTHYNNGVLLIAAAGNAGDSSYSYPASYDSVMSVAAVDSNLDHAAFSQYTDQVEISGPGEAILSTVTVGEGRLADITIGGQSYFSNGVVPHNRLTPSGTSYAPAPINASATGALAECTVNGTSFSCGNMANKICLVERVGNQGSSYPEINSTKACKTAGAKGIIVYSNSALPGLQNPFLVDANSDITVPSVSVDRATGLALKAKLGQSTTVSNQGNQDYEYYNGTSMATPHVSGVATLVWSYHPECSASQVRAALNATADDLSVAGRDNQTGYGMINAVAAKAYLDESCTGP 435
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430     


Chain B from PDB  Type:PROTEIN  Length:436
 aligned with Q65Z69_9GAMM | Q65Z69 from UniProtKB/TrEMBL  Length:817

    Alignment length:436
                                   154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574      
         Q65Z69_9GAMM   145 AETTPWGQTFVGATVLSDSQAGNRTICIIDSGYDRSHNDLNANNVTGTNNSGTGNWYQPGNNNAHGTHVAGTIAAIANNEGVVGVMPNQNANIHIVKVFNEAGWGYSSSLVAAIDTCVNSGGANVVTMSLGGSGSTTTERNALNTHYNNGVLLIAAAGNAGDSSYSYPASYDSVMSVAAVDSNLDHAAFSQYTDQVEISGPGEAILSTVTVGEGRLADITIGGQSYFSNGVVPHNRLTPSGTSYAPAPINASATGALAECTVNGTSFSCGNMANKICLVERVGNQGSSYPEINSTKACKTAGAKGIIVYSNSALPGLQNPFLVDANSDITVPSVSVDRATGLALKAKLGQSTTVSNQGNQDYEYYNGTSMATPHVSGVATLVWSYHPECSASQVRAALNATADDLSVAGRDNQTGYGMINAVAAKAYLDESCTGPT 580
               SCOP domains d1wvmb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1wvmB01 B:1-214,B:360-436  [code=3.40.50.200, no name defined]                                                                                                                                                        1wvmB02 B:215-359  [code=3.50.30.30, no name defined]                                                                                            1wvmB01 B:1-214,B:360-436  [code=3.40.50.200, no name defined]                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhh........hhhh.eeeeee.............eeee................hhhhhhhhhhhh.....ee.........eeeeee.ee..ee....hhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhh..eeeee.................eeeeeee...............eeeeee...eeee.....eeeeeeee..ee.hhhh.ee.eeeeee..eeee.....eeeeeeeeeeee..eee......eeeeee.........hhhhhhhhhhhh...eeeee...........eee.........eeeehhhhhhhhhhhh..eeeeeeeeee.eeee.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.................hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wvm B   1 AETTPWGQTFVGATVLSDSQAGNRTICIIDSGYDRSHNDLNANNVTGTNNSGTGNWYQPGNNNAHGTHVAGTIAAIANNEGVVGVMPNQNANIHIVKVFNEAGWGYSSSLVAAIDTCVNSGGANVVTMSLGGSGSTTTERNALNTHYNNGVLLIAAAGNAGDSSYSYPASYDSVMSVAAVDSNLDHAAFSQYTDQVEISGPGEAILSTVTVGEGRLADITIGGQSYFSNGVVPHNRLTPSGTSYAPAPINASATGALAECTVNGTSFSCGNMANKICLVERVGNQGSSYPEINSTKACKTAGAKGIIVYSNSALPGLQNPFLVDANSDITVPSVSVDRATGLALKAKLGQSTTVSNQGNQDYEYYNGTSMATPHVSGVATLVWSYHPECSASQVRAALNATADDLSVAGRDNQTGYGMINAVAAKAYLDESCTGPT 436
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430      


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1wvm C   1 FxLf   4
                             | |
                             2-CSI
                               4-PHA


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1wvm D   1 FxLf   4
                             | |
                             | |
                             2-CSI
                               4-PHA
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q65Z69_9GAMM | Q65Z69)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/TrEMBL
        Q65Z69_9GAMM | Q65Z69: 1v6c 1y9z

(-) Related Entries Specified in the PDB File

1v6c THE SAME PROTEIN AT 1.78 A RESOLUTION
1y9z THE SAME PROTEIN AT 1.40 A RESOLUTION