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(-) Description

Title :  CRYSTAL STRUCTURE OF DE NOVO DESIGNED SERINE HYDROLASE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET OR165
 
Authors :  A. Kuzin, S. Lew, J. Seetharaman, M. Maglaqui, R. Xiao, E. Kohan, S. Raja J. K. Everett, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northe Structural Genomics Consortium (Nesg)
Date :  08 May 12  (Deposition) - 30 May 12  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, De Novo Design, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Rajagopalan, C. Wang, K. Yu, A. P. Kuzin, F. Richter, S. Lew, A. E. Miklos, M. L. Matthews, J. Seetharaman, M. Su, J. F. Hunt, B. F. Cravatt, D. Baker
Design Of Activated Serine-Containing Catalytic Triads With Atomic-Level Accuracy.
Nat. Chem. Biol. V. 10 386 2014
PubMed-ID: 24705591  |  Reference-DOI: 10.1038/NCHEMBIO.1498

(-) Compounds

Molecule 1 - DE NOVO DESIGNED SERINE HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTIFICIAL GENE
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1CXM2Mod. Amino AcidN-CARBOXYMETHIONINE
2LMU2Ligand/IonDODECYL-ALPHA-D-MALTOSIDE
3MSE14Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:21 , PHE A:62 , TRP A:83 , TRP A:98 , ASN A:143 , ALA A:144 , SER A:146 , ARG A:166 , SER A:167 , SER A:173 , PHE A:176 , GLY A:181 , LEU A:184 , PEG A:302 , HOH A:415 , HOH A:428 , HOH A:461 , ARG B:126BINDING SITE FOR RESIDUE LMU A 301
2AC2SOFTWAREPHE A:62 , HIS A:94 , TRP A:98 , PRO A:145 , SER A:146 , HIS A:147 , LMU A:301BINDING SITE FOR RESIDUE PEG A 302
3AC3SOFTWAREARG A:126 , PHE B:62 , ILE B:79 , LEU B:80 , TRP B:83 , ASN B:143 , ALA B:144 , SER B:146 , ARG B:166 , SER B:167 , SER B:173 , HOH B:443BINDING SITE FOR RESIDUE LMU B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F2V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F2V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F2V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F2V)

(-) Exons   (0, 0)

(no "Exon" information available for 4F2V)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.............hhhhhhhhhhhhhhh...hhhhhhh....hhhhh...........hhhhheee...eeehhhhhhhhhhhhh......eee..hhhhhh.........eeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f2v A   1 mKQYLELmQKVLDEGTQKNDRTGTGTLSIFGHQmRFNLQDGFPLVTTKRCHLRSIIHLLLWFLQGDTNIAYLHENNVTILDEWADENGDLGPVHGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKmANAPSHAFFQFYVADGKLSCQLYARSEDVFLSLPFAIASGALLVHmmAQQCDLEVGDFVmTGGDTHLYSNHmDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPV 262
                            |      |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  
                            |      8-MSE                    34-MSE                                                                                                    141-MSE                                       187-MSE       201-MSE     213-MSE                                             
                            1-CXM                                                                                                                                                                                    188-MSE                                                                      


Chain B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheee....eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhhh....hhhhhh....hhhhh....hhhhhhee.....eehhhhhhhhhhhhh.....eeee.................eeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f2v B   1 mKQYLELmQKVLDEGTQKNGTGTLSIFGHQmRFNLQDGFPLVTTKRCHLRSIIHLLLWFLQGDTNIAYLHENNVTILDEWADDLHGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKmANAPSHAFFQFYVADGKLSCQLYARSEDVFLSLPFAIASGALLVHmmAQQCDLEVGDFVmTGGDTHLYSNHmDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAP 261
                            |      |10        23        33|       43        53        63        73        83 ||||   99       109       119       129       139 |     149       159       169       179       189       199 |     209   |   219       229       239       249       259  
                            1-CXM  8-MSE     19|         34-MSE                                             85|||                                            141-MSE                                       187-MSE       201-MSE     213-MSE                                            
                                              23                                                             89||                                                                                           188-MSE                                                                     
                                                                                                              90|                                                                                                                                                                       
                                                                                                               94
   Legend:   → Mismatch (orange background)
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    → 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 4F2V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F2V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F2V)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  4f2v
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 Related Entries

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

UniProtKB/Swiss-Prot
        TYSY_ECOLI | P0A884: 1aiq 1ajm 1an5 1aob 1axw 1bdu 1bid 1bjg 1bq1 1bq2 1ddu 1dna 1ev5 1ev8 1evf 1evg 1f4b 1f4c 1f4d 1f4e 1f4f 1f4g 1ffl 1fwm 1jg0 1jtq 1jtu 1jut 1kce 1kzi 1kzj 1nce 1qqq 1syn 1tdu 1tjs 1tlc 1tls 1trg 1tsd 1tsn 1tys 1zpr 2a9w 2bbq 2ftn 2fto 2ftq 2g8x 2kce 2tsc 2vet 2vf0 3b5b 3b9h 3bfi 3bgx 3bhl 3bhr 3tms 4gev 4isk 4knz

(-) Related Entries Specified in the PDB File

1bq2 HOMOLOGUE 96.2% RELATED ID: NESG-OR165 RELATED DB: TARGETTRACK