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(-) Description

Title :  CRYSTAL STRUCTURE OF CARBOXYPEPTIDASE FROM THERMUS THERMOPHILUS
 
Authors :  M. Okai, K. Nagata, M. Tanokura, Riken Structural Genomics/Proteom Initiative (Rsgi)
Date :  29 Dec 16  (Deposition) - 22 Feb 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Carboxypeptidase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Okai, A. Yamamura, K. Hayakawa, S. Tsutsui, K. I. Miyazono, W. C. Lee K. Nagata, Y. Inoue, M. Tanokura
Insight Into The Transition Between The Open And Closed Conformations Of Thermus Thermophilus Carboxypeptidase.
Biochem. Biophys. Res. V. 484 787 2017 Commun.
PubMed-ID: 28161633  |  Reference-DOI: 10.1016/J.BBRC.2017.01.167

(-) Compounds

Molecule 1 - THERMOSTABLE CARBOXYPEPTIDASE 1
    Chains: A, B, C
    EC Number: 3.4.17.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TTHA0270
    Organism Scientific: THERMUS THERMOPHILUS HB8
    Organism Taxid: 300852
    Strain: HB8
    Synonym: TTHCP1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2ZN3Ligand/IonZINC ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:465 , ARG A:468binding site for residue GOL A 801
2AC2SOFTWAREGLN A:31 , HIS A:40 , ARG A:43 , ALA A:44 , MET A:47binding site for residue GOL A 802
3AC3SOFTWAREGLN A:14 , TRP A:90 , GLY A:293 , THR A:294 , ASP A:298binding site for residue GOL A 803
4AC4SOFTWAREHIS A:276 , HIS A:280 , GLU A:306binding site for residue ZN A 804
5AC5SOFTWAREHIS B:276 , HIS B:280 , GLU B:306binding site for residue ZN B 601
6AC6SOFTWAREGLN C:14 , TRP C:90 , GLY C:293 , THR C:294 , PRO C:295 , ASP C:298binding site for residue GOL C 601
7AC7SOFTWAREHIS C:276 , HIS C:280 , GLU C:306 , TYR C:430binding site for residue ZN C 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5WVU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:205 -Pro A:206
2Arg C:205 -Pro C:206

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5WVU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5WVU)

(-) Exons   (0, 0)

(no "Exon" information available for 5WVU)

(-) 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:510
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5wvu A   1 MTPEAAYQNLLEFQRETAYLASLGALAAWDQRTMIPKKGHEHRARQMAALARLLHQRMTDPRIGEWLEKVEGSPLVQDPLSDAAVNVREWRQAYERARAIPERLAVELAQAESEAESFWEEARPRDDWRGFLPYLKRVYALTKEKAEVLFALPPAPGDPPYGELYDALLDGYEPGMRARELLPLFAELKEGLKGLLDRILGSGKRPDTSILHRPYPVEAQRRFALELLSACGYDLEAGRLDPTAHPFEIAIGPGDVRITTRYYEDFFNAGIFGTLHEMGHALYEQGLPKEHWGTPRGDAVSLGVHESQSRTWENLVGRSLGFWERFFPRAREVFASLGDVSLEDFHFAVNAVEPSLIRVEADEVTYNLHILVRLELELALFRGELSPEDLPEAWAEKYRDHLGVAPKDYKDGVMQDVHWAGGLFGYFPTYTLGNLYAAQFFQKAEAELGPLEPRFARGEFQPFLDWTRARIHAEGSRFRPRVLVERVTGEAPSARPFLAYLEKKYAALYG 510
                                    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       440       450       460       470       480       490       500       510


Chain B from PDB  Type:PROTEIN  Length:510
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhh.hhh.eeeee....eeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5wvu B   1 MTPEAAYQNLLEFQRETAYLASLGALAAWDQRTMIPKKGHEHRARQMAALARLLHQRMTDPRIGEWLEKVEGSPLVQDPLSDAAVNVREWRQAYERARAIPERLAVELAQAESEAESFWEEARPRDDWRGFLPYLKRVYALTKEKAEVLFALPPAPGDPPYGELYDALLDGYEPGMRARELLPLFAELKEGLKGLLDRILGSGKRPDTSILHRPYPVEAQRRFALELLSACGYDLEAGRLDPTAHPFEIAIGPGDVRITTRYYEDFFNAGIFGTLHEMGHALYEQGLPKEHWGTPRGDAVSLGVHESQSRTWENLVGRSLGFWERFFPRAREVFASLGDVSLEDFHFAVNAVEPSLIRVEADEVTYNLHILVRLELELALFRGELSPEDLPEAWAEKYRDHLGVAPKDYKDGVMQDVHWAGGLFGYFPTYTLGNLYAAQFFQKAEAELGPLEPRFARGEFQPFLDWTRARIHAEGSRFRPRVLVERVTGEAPSARPFLAYLEKKYAALYG 510
                                    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       440       450       460       470       480       490       500       510


Chain C from PDB  Type:PROTEIN  Length:510
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhh.hhhhh.eee.....eeeee..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5wvu C   1 MTPEAAYQNLLEFQRETAYLASLGALAAWDQRTMIPKKGHEHRARQMAALARLLHQRMTDPRIGEWLEKVEGSPLVQDPLSDAAVNVREWRQAYERARAIPERLAVELAQAESEAESFWEEARPRDDWRGFLPYLKRVYALTKEKAEVLFALPPAPGDPPYGELYDALLDGYEPGMRARELLPLFAELKEGLKGLLDRILGSGKRPDTSILHRPYPVEAQRRFALELLSACGYDLEAGRLDPTAHPFEIAIGPGDVRITTRYYEDFFNAGIFGTLHEMGHALYEQGLPKEHWGTPRGDAVSLGVHESQSRTWENLVGRSLGFWERFFPRAREVFASLGDVSLEDFHFAVNAVEPSLIRVEADEVTYNLHILVRLELELALFRGELSPEDLPEAWAEKYRDHLGVAPKDYKDGVMQDVHWAGGLFGYFPTYTLGNLYAAQFFQKAEAELGPLEPRFARGEFQPFLDWTRARIHAEGSRFRPRVLVERVTGEAPSARPFLAYLEKKYAALYG 510
                                    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       440       450       460       470       480       490       500       510
   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 ; only for superseded entry 1WGZ: 1,3)

(no "SCOP Domain" information available for 5WVU, only for superseded entry 1WGZ replaced by 5WVU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5WVU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5WVU)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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