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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DEPH COMPLEX WITH DIMETHYL-FK228
 
Authors :  J. Li, C. Wang, Z. M. Zhang, J. H. Zhou, E. Cheng
Date :  14 Mar 13  (Deposition) - 05 Mar 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,H,I
Biol. Unit 1:  A,I  (1x)
Biol. Unit 2:  B,H  (1x)
Keywords :  Disulfide Bond Formation, Fk228, Depsipeptide, Fad-Dependent Oxidoreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Li, C. Wang, Z. M. Zhang, Y. Q. Cheng, J. Zhou
The Structural Basis Of An Nadp+-Independent Dithiol Oxidas In Fk228 Biosynthesis.
Sci Rep V. 4 4145 2014
PubMed-ID: 24553401  |  Reference-DOI: 10.1038/SREP04145

(-) Compounds

Molecule 1 - DEPH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEPH
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536
    Strain: NO. 968
 
Molecule 2 - DIMETHYL FK228
    Chains: H, I
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHI
Biological Unit 1 (1x): A  I
Biological Unit 2 (1x):  BH 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 18)

Asymmetric Unit (9, 18)
No.NameCountTypeFull Name
10602Mod. Amino AcidS-METHYL-D-CYSTEINE
21KC2Mod. Amino Acid(3S)-7-METHYLSULFANYL-3-OXIDANYL-HEPT-4-ENOIC ACID
3CL2Ligand/IonCHLORIDE ION
4DBU2Mod. Amino Acid(2Z)-2-AMINOBUT-2-ENOIC ACID
5DVA2Mod. Amino AcidD-VALINE
6EDO4Ligand/Ion1,2-ETHANEDIOL
7FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
8GOL1Ligand/IonGLYCEROL
9PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (7, 8)
No.NameCountTypeFull Name
10601Mod. Amino AcidS-METHYL-D-CYSTEINE
21KC1Mod. Amino Acid(3S)-7-METHYLSULFANYL-3-OXIDANYL-HEPT-4-ENOIC ACID
3CL-1Ligand/IonCHLORIDE ION
4DBU1Mod. Amino Acid(2Z)-2-AMINOBUT-2-ENOIC ACID
5DVA1Mod. Amino AcidD-VALINE
6EDO2Ligand/Ion1,2-ETHANEDIOL
7FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
8GOL-1Ligand/IonGLYCEROL
9PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (7, 8)
No.NameCountTypeFull Name
10601Mod. Amino AcidS-METHYL-D-CYSTEINE
21KC1Mod. Amino Acid(3S)-7-METHYLSULFANYL-3-OXIDANYL-HEPT-4-ENOIC ACID
3CL-1Ligand/IonCHLORIDE ION
4DBU1Mod. Amino Acid(2Z)-2-AMINOBUT-2-ENOIC ACID
5DVA1Mod. Amino AcidD-VALINE
6EDO2Ligand/Ion1,2-ETHANEDIOL
7FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
8GOL1Ligand/IonGLYCEROL
9PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:55 , SER A:57 , HIS A:58 , ALA A:59 , ILE A:77 , ASP A:78 , ALA A:79 , GLY A:80 , ALA A:81 , ARG A:82 , ARG A:83 , ASN A:84 , SER A:90 , HIS A:91 , ASP A:123 , SER A:124 , VAL A:125 , ALA A:153 , PHE A:154 , GLY A:155 , ASP A:158 , CYS A:180 , HIS A:181 , SER A:273 , SER A:274 , GLY A:310 , ASP A:311 , GLY A:317 , THR A:318 , VAL A:319 , HOH A:505 , HOH A:506 , HOH A:517 , HOH A:520 , HOH A:531 , HOH A:545 , HOH A:551 , HOH A:578 , HOH A:647BINDING SITE FOR RESIDUE FAD A 401
02AC2SOFTWAREHIS A:176 , CYS A:177 , HIS A:181BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWAREPHE A:86 , ASP A:158 , LEU A:160 , GLU A:167 , HOH A:539BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWAREALA A:114 , TYR A:115 , HOH B:515 , HOH B:580BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREVAL A:238 , ARG A:239 , ASP A:240 , ARG A:257 , HOH A:532BINDING SITE FOR RESIDUE PO4 A 405
06AC6SOFTWAREILE B:54 , GLY B:55 , SER B:57 , HIS B:58 , ALA B:59 , ILE B:77 , ASP B:78 , ALA B:79 , GLY B:80 , ALA B:81 , ARG B:83 , ASN B:84 , SER B:90 , HIS B:91 , ASP B:123 , SER B:124 , VAL B:125 , PHE B:154 , GLY B:155 , ASP B:158 , CYS B:180 , HIS B:181 , SER B:273 , SER B:274 , GLY B:310 , ASP B:311 , GLY B:317 , THR B:318 , VAL B:319 , CL B:402 , HOH B:501 , HOH B:502 , HOH B:510 , HOH B:512 , HOH B:516 , HOH B:531 , HOH B:543 , HOH B:568BINDING SITE FOR RESIDUE FAD B 401
07AC7SOFTWAREHIS B:176 , CYS B:177 , HIS B:181 , FAD B:401BINDING SITE FOR RESIDUE CL B 402
08AC8SOFTWAREILE A:94 , GLN A:96 , ILE B:94 , GLY B:95 , GLN B:96BINDING SITE FOR RESIDUE EDO B 403
09AC9SOFTWAREHOH A:634 , TYR B:115 , HOH B:540BINDING SITE FOR RESIDUE EDO B 404
10BC1SOFTWAREPRO B:197 , TYR B:200 , GLN B:226 , ARG B:241 , ALA B:254BINDING SITE FOR RESIDUE GOL B 405
11BC2SOFTWARELEU A:328 , ILE A:331 , ARG A:335 , CYS B:177 , ASP B:255 , ARG B:257 , PRO B:288 , THR B:313 , HIS B:314 , ARG B:315 , GLY B:316 , HOH H:101 , HOH H:102 , HOH H:103 , HOH H:104BINDING SITE FOR CHAIN H OF DIMETHYL FK228
12BC3SOFTWARECYS A:177 , TYR A:179 , MET A:267 , HIS A:314 , ARG A:315 , GLY A:316 , LEU B:328 , ILE B:331 , ARG B:335 , HOH I:101BINDING SITE FOR CHAIN I OF DIMETHYL FK228

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JNA)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhh...eeeee..eeeeeee..eeeeee....eeeeeeeee...eeee......hhhhh...ee.hhhhhhhhhheeeeeee....hhhhhhhhh...eeeeee.......hhhhhhhhhhh..eee...eeeee...eeee....eee..eeee..eeee..hhhhhh...eeee..eeee............eee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jna A  45 SPMLFDVIVIGGSHAGQSAALQIARARRRVLVIDAGARRNRFASQSHGVIGQDGRSPDAIAADGKAQLLAYPNAQWREDSVVRAERSDAGYTLICASGQHYRACQLVLAFGVVDELPELEGLEERWGESVFHCPYCHGYELDGGRIGVLGSGPLSYLSAMLMPEWGQTVFLTDASFEPDEEQREALARRGVEIVRDRIARIVDRATVELADGRRIAFDGLFTMNRMRLSSPVAEQLGCAIEEGPLGPYVRTDDAMETSTPGVFACGDITHRGGTVALAIGNGALAGIAAHRKLVFG 340
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334      


Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhh...eeeee..eeeeee....eeeee....eeeeeeeee...eeee.....hhhhhh...ee.hhhhhhhhhheeeeeee....hhhhhhhhh...eeeeee.......hhhhhhhhhhh..eee...eeeee...eeee....eee..eeee..eeee..hhhhhh...eeee..eeee............eee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jna B  48 LFDVIVIGGSHAGQSAALQIARARRRVLVIDAGARRNRFASQSHGVIGQDGRSPDAIAADGKAQLLAYPNAQWREDSVVRAERSDAGYTLICASGQHYRACQLVLAFGVVDELPELEGLEERWGESVFHCPYCHGYELDGGRIGVLGSGPLSYLSAMLMPEWGQTVFLTDASFEPDEEQREALARRGVEIVRDRIARIVDRATVELADGRRIAFDGLFTMNRMRLSSPVAEQLGCAIEEGPLGPYVRTDDAMETSTPGVFACGDITHRGGTVALAIGNGALAGIAAHRKLVFG 340
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337   


Chain H from PDB  Type:PROTEIN  Length:5
                                     
               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
                 4jna H   1 xxxtV   5
                            |||| 
                            1-1KC
                             2-DVA
                              3-060
                               4-DBU


Chain I from PDB  Type:PROTEIN  Length:5
                                     
               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
                 4jna I   1 xxxtV   5
                            |||| 
                            |||| 
                            1-1KC
                             2-DVA
                              3-060
                               4-DBU
   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)

(no "SCOP Domain" information available for 4JNA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

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        A4ZPY8_CHRVL | A4ZPY8: 4jn9 4nte

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4jn9