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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT PROTEIN YHFX FROM ESCHERICHIA COLI
 
Authors :  A. A. Fedorov, E. V. Fedorov, D. F. Xiang, F. M. Raushel, S. C. Almo
Date :  24 Apr 13  (Deposition) - 21 May 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  D-Serine Dehydratase Fold, Protein Yhfx, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, D. F. Xiang, F. M. Raushel, S. C. Almo
Crystal Structure Of The Pyridoxal-5'-Phosphate Dependent Protein Yhfx From Escherichia Coli
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YHFX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YHFX, B3381, JW3344
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 12)

Asymmetric Unit (6, 12)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CL1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
5MSE4Mod. Amino AcidSELENOMETHIONINE
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 22)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CL-1Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
5MSE8Mod. Amino AcidSELENOMETHIONINE
6SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:299 , ARG A:301 , ARG A:351 , GLN A:353 , HOH A:592 , HOH A:658 , HOH A:699BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWARETYR A:86 , ARG A:93 , GLN A:102 , GLN A:112 , ALA A:116 , GLN A:119 , HOH A:719BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWARESER A:15 , ASN A:314 , GLN A:315 , ILE A:317BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWARELYS A:43 , LYS A:223 , HOH A:603BINDING SITE FOR RESIDUE GOL A 404
5AC5SOFTWARETHR A:311 , PRO A:312 , GLU A:313 , HOH A:570BINDING SITE FOR RESIDUE CL A 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:104 -Leu A:105
2Phe A:193 -Pro A:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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    
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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:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhh.ee.ee.hhhh.hhhhhhhhhh.....eee.hhhhhhhhhhh...eeee......hhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhh...eeeeeeee.............ee..hhhhhhhhhhhh..eeeeeee....eeee....eeeehhhhhhhhhhhhhhhh......eee........hhhhhhhh...ee..hhhhhh.hhhhh.........eeeeeeeeeee..eeeee...........eeeeee....eeeeee...........eeee........eeee....hhhhh..eeeeeehhhhh..eeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbx A   0 xmFVEALkRQNPALISAALSLWQQGKIAPDSWVIDVDQILENGKRLIETARLYGIELYLmTkQFGRNPWLAEKLLALGYSGIVAVDYKEARVmRRAGLPVAHQGHLVQIPCHQVADAVEQGTDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDDDFLYPGQESGFALKVLPEIVAEIQNLPGLHLAGLTHFPCLLWDEAVGKVLPTPNLHTLIQARDQLAKSGIALEQLNAPSATSCTSLPLLAQYGVTHAEPGHALTGTIPANQQGDQPERIAmLWLSEISHHFRGDSYCYGGGYYRRGHAQHALVFTPENQKITETNLKTVDDSSIDYTLPLAGEFPVSSAVVLCFRTQIFVTRSDVVLVSGIHRGEPEIVGRYDSLGNSLG 386
                            ||     | 9        19        29        39        49        59 |      69        79        89  |     99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       
                            ||     7-LLP                                              59-MSE                           92-MSE                                                                                                                                                                                  277-MSE                                                                                                         
                            0-ACE                                                       61-LLP                                                                                                                                                                                                                                                                                                                                 
                             1-MSE
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  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 4KBX)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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