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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PROTEASE (BDI_1141) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Oct 09  (Deposition) - 24 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  B  (2x)
Keywords :  Putative Protease, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Proteases (Yp_001302526. 1) From Parabacteroides Distasonis Atcc 8503 At 2. 00 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BDI_1141
    Organism Scientific: PARABACTEROIDES DISTASONIS ATCC 8503
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152
    Synonym: CONSERVED HYPOTHETICAL EXPORTED PROTEIN, POSSIBLE ATP/GTP- BINDING

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 43)

Asymmetric Unit (3, 43)
No.NameCountTypeFull Name
1GOL21Ligand/IonGLYCEROL
2MSE16Mod. Amino AcidSELENOMETHIONINE
3PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 23)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 20)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3PO43Ligand/IonPHOSPHATE ION
Biological Unit 3 (3, 40)
No.NameCountTypeFull Name
1GOL18Ligand/IonGLYCEROL
2MSE16Mod. Amino AcidSELENOMETHIONINE
3PO46Ligand/IonPHOSPHATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:31 , GLU A:51 , TYR A:134 , HOH A:784 , HOH A:944 , HOH A:1009 , LYS B:241BINDING SITE FOR RESIDUE PO4 A 2
02AC2SOFTWAREGLU A:172 , GLY A:173 , LYS A:196 , HOH A:1067BINDING SITE FOR RESIDUE PO4 A 3
03AC3SOFTWARELYS A:241 , HOH A:765 , HOH A:781 , LYS B:31 , GLU B:51 , TYR B:134BINDING SITE FOR RESIDUE PO4 A 5
04AC4SOFTWAREGLN A:44 , TYR A:146 , ALA A:148 , LEU A:149 , ASP A:150 , TYR A:292 , HOH A:879BINDING SITE FOR RESIDUE GOL A 7
05AC5SOFTWARETYR A:29 , LYS A:34 , MSE A:50 , GLU A:157 , HOH A:601 , HOH A:698 , HOH A:704 , HOH A:1077BINDING SITE FOR RESIDUE GOL A 8
06AC6SOFTWAREGOL A:10 , THR A:37 , HIS A:39 , GLU A:45 , HOH A:812 , HOH A:918 , SER B:383BINDING SITE FOR RESIDUE GOL A 9
07AC7SOFTWAREGOL A:9 , GLU A:45 , ARG A:47 , HOH A:650 , HOH A:977 , LYS B:375 , SER B:383 , HOH B:650 , HOH B:692BINDING SITE FOR RESIDUE GOL A 10
08AC8SOFTWAREPRO A:230 , SER A:231 , ASP A:339 , HOH A:655 , HOH A:968 , HIS B:81 , LYS B:94 , HOH B:563 , HOH B:652 , HOH B:1009BINDING SITE FOR RESIDUE GOL A 15
09AC9SOFTWAREPRO A:105 , ARG A:106 , PHE A:107 , GLU A:119BINDING SITE FOR RESIDUE GOL A 18
10BC1SOFTWAREGLY A:179 , LEU A:180 , HOH A:545BINDING SITE FOR RESIDUE GOL A 19
11BC2SOFTWAREHIS A:57 , GLU A:128 , LEU A:129 , GLN B:465 , GLU B:466 , VAL B:468BINDING SITE FOR RESIDUE GOL A 21
12BC3SOFTWAREASN A:217 , GLY A:334 , HIS A:335 , LEU A:373 , GLN A:499 , HOH A:678 , HOH A:715BINDING SITE FOR RESIDUE GOL A 528
13BC4SOFTWAREASP A:97 , PHE A:100 , HOH A:992 , HOH A:1090BINDING SITE FOR RESIDUE GOL A 529
14BC5SOFTWARELEU A:315 , LEU A:349 , VAL A:351 , LEU A:362 , SER A:363 , HOH A:775 , HOH A:878 , HOH A:985BINDING SITE FOR RESIDUE GOL A 530
15BC6SOFTWAREGLU A:163 , LYS A:165 , ARG A:203 , HOH A:886BINDING SITE FOR RESIDUE GOL A 531
16BC7SOFTWAREHIS B:275 , ASN B:279 , HOH B:705 , HOH B:732 , HOH B:929BINDING SITE FOR RESIDUE PO4 B 1
17BC8SOFTWARESER A:383 , HOH A:716 , GLU B:45 , ARG B:47 , GOL B:528 , HOH B:706 , HOH B:718 , HOH B:865BINDING SITE FOR RESIDUE PO4 B 4
18BC9SOFTWAREGLU B:172 , GLY B:173 , LYS B:196 , HOH B:565 , HOH B:1021BINDING SITE FOR RESIDUE PO4 B 6
19CC1SOFTWAREGLN B:44 , TYR B:146 , ALA B:148 , LEU B:149 , ASP B:150 , TYR B:292 , HOH B:1026BINDING SITE FOR RESIDUE GOL B 11
20CC2SOFTWAREPRO B:105 , ARG B:106 , PHE B:107 , GLU B:119 , HOH B:1071 , HOH B:1088BINDING SITE FOR RESIDUE GOL B 12
21CC3SOFTWARETYR B:29 , LYS B:34 , MSE B:50 , GLU B:157 , HOH B:667BINDING SITE FOR RESIDUE GOL B 13
22CC4SOFTWAREGLU A:466 , GLN A:467 , HIS B:57 , GLU B:128 , LEU B:129 , HOH B:590 , HOH B:656BINDING SITE FOR RESIDUE GOL B 14
23CC5SOFTWAREHIS A:81 , LYS A:94 , HOH A:549 , HOH A:557 , HOH A:598 , PRO B:230 , SER B:231 , ASP B:339 , HOH B:619 , HOH B:710BINDING SITE FOR RESIDUE GOL B 16
24CC6SOFTWAREPHE B:213 , GLN B:214 , GLU B:439 , HOH B:994BINDING SITE FOR RESIDUE GOL B 17
25CC7SOFTWAREPRO B:308 , LEU B:362 , SER B:363 , HOH B:795 , HOH B:942BINDING SITE FOR RESIDUE GOL B 20
26CC8SOFTWARESER A:383 , GLU A:385 , PO4 B:4 , THR B:37 , HIS B:39 , GLU B:45 , HOH B:596 , HOH B:822BINDING SITE FOR RESIDUE GOL B 528
27CC9SOFTWAREASP A:359 , THR A:368 , GLU A:387 , HOH A:791 , HIS B:192 , ASP B:193BINDING SITE FOR RESIDUE GOL B 529

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KD4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KD4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KD4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KD4)

(-) Exons   (0, 0)

(no "Exon" information available for 3KD4)

(-) 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:505
 aligned with A6LB40_PARD8 | A6LB40 from UniProtKB/TrEMBL  Length:527

    Alignment length:505
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522     
         A6LB40_PARD8    23 AASEAEYGKVSKAWTLHADGSQEYRSSMELTLFTHTAMNSTYGESFIVYNPDFQTLKIHSSYTRQKDGTIVKTPDNAFVEVLPRFAADAPAYNQLKEMVVVHTGLELGATIYLDYSIITKPGYYPALDINERLQETSPVKECKVSISVPEGTPLACGLYGSPVKAVEESHDGIKEVHWTLRNIPASSREAFQPKNREASPHLVASTYPSGKAALATLDKRLKESQGYESKTFAQFLTDKSGNEQEKVNIIRDHILNNLSTCPIPMAMTGYTVRDIDTVLRSAYGTPLEIAQLLNVMLNAAGIPSEVLAVYPGHLDTDACGLAAIQTLAVKATVDGKDQYLSASPLTNRGGLDKVVSLSGTSIEIETTPIQIKESRSVAISADQAKDGFAICVLPAISAGIDSWGMSALNSKRSNLFELPSLIREEVTYTVTPAEGMKLQTSTQEQVISKPFGKVTRTITPRGNTIEVVRTIELNKQQFTPAEYSDVRSLIHEWTNPDNRVLLFSL 527
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee.....eeeeeeeeeee.hhhhhhhhh.eeeeee....eeeeeeeeeee.....eee.hhh.eeee.hhhhh.hhhhh..eeeeee........eeeeeeeeee........eeeee......eeeeeeeeeee.....eeeee......eeeee..eeeeeeeeeee.................eeeee...hhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhee...hhhhhh....hhhhhhhhheehhhhhhhhhhhhhhhh...eeeeeeee...hhhhh......eeeeeeee..eeeee...hhhhhh..eeeee....ee......eeeeeeeeeee.hhhhh..eeeee.....hhhhhh............ee....eeeeeeeeeee....ee......eeeee..eeeeeeeeee..eeeeeeeeee...eehhhhhhhhhhhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kd4 A  23 AASEAEYGKVSKAWTLHADGSQEYRSSmELTLFTHTAmNSTYGESFIVYNPDFQTLKIHSSYTRQKDGTIVKTPDNAFVEVLPRFAADAPAYNQLKEmVVVHTGLELGATIYLDYSIITKPGYYPALDINERLQETSPVKECKVSISVPEGTPLACGLYGSPVKAVEESHDGIKEVHWTLRNIPASSREAFQPKNREASPHLVASTYPSGKAALATLDKRLKESQGYESKTFAQFLTDKSGNEQEKVNIIRDHILNNLSTCPIPmAmTGYTVRDIDTVLRSAYGTPLEIAQLLNVmLNAAGIPSEVLAVYPGHLDTDACGLAAIQTLAVKATVDGKDQYLSASPLTNRGGLDKVVSLSGTSIEIETTPIQIKESRSVAISADQAKDGFAICVLPAISAGIDSWGmSALNSKRSNLFELPSLIREEVTYTVTPAEGmKLQTSTQEQVISKPFGKVTRTITPRGNTIEVVRTIELNKQQFTPAEYSDVRSLIHEWTNPDNRVLLFSL 527
                                    32        42       |52       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282    | |292       302       312     | 322       332       342       352       362       372       382       392       402       412       422    |  432       442       452     | 462       472       482       492       502       512       522     
                                                      50-MSE    60-MSE                                                     120-MSE                                                                                                                                                                287-MSE                        318-MSE                                                                                                      427-MSE                        458-MSE                                                                 
                                                                                                                                                                                                                                                                                                    289-MSE                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:505
 aligned with A6LB40_PARD8 | A6LB40 from UniProtKB/TrEMBL  Length:527

    Alignment length:505
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522     
         A6LB40_PARD8    23 AASEAEYGKVSKAWTLHADGSQEYRSSMELTLFTHTAMNSTYGESFIVYNPDFQTLKIHSSYTRQKDGTIVKTPDNAFVEVLPRFAADAPAYNQLKEMVVVHTGLELGATIYLDYSIITKPGYYPALDINERLQETSPVKECKVSISVPEGTPLACGLYGSPVKAVEESHDGIKEVHWTLRNIPASSREAFQPKNREASPHLVASTYPSGKAALATLDKRLKESQGYESKTFAQFLTDKSGNEQEKVNIIRDHILNNLSTCPIPMAMTGYTVRDIDTVLRSAYGTPLEIAQLLNVMLNAAGIPSEVLAVYPGHLDTDACGLAAIQTLAVKATVDGKDQYLSASPLTNRGGLDKVVSLSGTSIEIETTPIQIKESRSVAISADQAKDGFAICVLPAISAGIDSWGMSALNSKRSNLFELPSLIREEVTYTVTPAEGMKLQTSTQEQVISKPFGKVTRTITPRGNTIEVVRTIELNKQQFTPAEYSDVRSLIHEWTNPDNRVLLFSL 527
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------DUF3857-3kd4B01 B:37-212                                                                                                                                                        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DUF3858-3kd4B03 B:410-525                                                                                           -- Pfam domains (1)
           Pfam domains (2) --------------DUF3857-3kd4B02 B:37-212                                                                                                                                                        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DUF3858-3kd4B04 B:410-525                                                                                           -- Pfam domains (2)
         Sec.struct. author ....eeeeeeeeeeee.....eeeeeeeeeee.hhhhhhhhh.eeeeee....eeeeeeeeeee.....eee.hhh.eeee.hhhhh.hhhhh..eeeeee........eeeeeeeeee........eeeee......eeeeeeeeeee.....eeeee......ee.....eeeeeeeeeee.................eeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhee...hhhhhh....hhhhhhhhheehhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhh.eeeeeeee..eeeee...hhhhhh..eeeee....ee......eeeeeeeeeeehhhhhh..eeeee.....hhhhhh............ee....eeeeeeeeeee....ee......eeeee..eeeeeeeeee..eeeeeeeeee...eehhhhhhhhhhhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kd4 B  23 AASEAEYGKVSKAWTLHADGSQEYRSSmELTLFTHTAmNSTYGESFIVYNPDFQTLKIHSSYTRQKDGTIVKTPDNAFVEVLPRFAADAPAYNQLKEmVVVHTGLELGATIYLDYSIITKPGYYPALDINERLQETSPVKECKVSISVPEGTPLACGLYGSPVKAVEESHDGIKEVHWTLRNIPASSREAFQPKNREASPHLVASTYPSGKAALATLDKRLKESQGYESKTFAQFLTDKSGNEQEKVNIIRDHILNNLSTCPIPmAmTGYTVRDIDTVLRSAYGTPLEIAQLLNVmLNAAGIPSEVLAVYPGHLDTDACGLAAIQTLAVKATVDGKDQYLSASPLTNRGGLDKVVSLSGTSIEIETTPIQIKESRSVAISADQAKDGFAICVLPAISAGIDSWGmSALNSKRSNLFELPSLIREEVTYTVTPAEGmKLQTSTQEQVISKPFGKVTRTITPRGNTIEVVRTIELNKQQFTPAEYSDVRSLIHEWTNPDNRVLLFSL 527
                                    32        42       |52       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282    | |292       302       312     | 322       332       342       352       362       372       382       392       402       412       422    |  432       442       452     | 462       472       482       492       502       512       522     
                                                      50-MSE    60-MSE                                                     120-MSE                                                                                                                                                                287-MSE                        318-MSE                                                                                                      427-MSE                        458-MSE                                                                 
                                                                                                                                                                                                                                                                                                    289-MSE
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  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 3KD4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KD4)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF3857] (1)
(-)
Clan: no clan defined [family: DUF3858] (1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3KD4)

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