4B2H - JenaLib

Title :   COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

Authors :   Y. Yu, B. Heidel, T. L. Parapugna, S. Wenderhold-Reeb, B. Song, H. Schoe M. Grininger, G. Noell

Date :   16 Jul 12 (Deposition) - 29 May 13 (Release) - 29 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A
Biol. Unit 1: A  (12x)

Keywords :   Flavoprotein, Biotechnological Application Of Dodecin Binding Properties, Flavin-Dna Ligand Hybrid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Yu, B. Heidel, T. L. Parapugna, S. Wenderhold-Reeb, B. Song, H. Schonherr, M. Grininger, G. Noll
The Flavoprotein Dodecin As A Redox Probe For Electron Transfer Through Dna.
Angew. Chem. Int. Ed. Engl. V. 52 4950 2013
PubMed-ID: 23532984 | Reference-DOI: 10.1002/ANIE.201208987

Compounds

Molecule 1 - DODECIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET22B
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	HALOBACTERIUM SALINARUM
	Organism Taxid	:	478009
	Other Details	:	LIGAND-BOUND FORM
	Other Details - Source	:	GERMAN COLLECTION OF MICROORGANISMS (DSM 671)
	Strain	:	R1

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Asymmetric Unit (5, 6)

No.	Name	Count	Type	Full Name
1	C3F	1	Ligand/Ion	3-[7,8-DIMETHYL-2,4-BIS(OXIDANYLIDENE)BENZO[G]PTERIDIN-10-YL]PROPYLCARBAMIC ACID
2	CL	1	Ligand/Ion	CHLORIDE ION
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	NA	2	Ligand/Ion	SODIUM ION
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 24)

No.	Name	Count	Type	Full Name
1	C3F	12	Ligand/Ion	3-[7,8-DIMETHYL-2,4-BIS(OXIDANYLIDENE)BENZO[G]PTERIDIN-10-YL]PROPYLCARBAMIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	SO4	12	Ligand/Ion	SULFATE ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:41 , HOH A:2059 , HOH A:2072 , HOH A:2073 , HOH A:2074	BINDING SITE FOR RESIDUE NA A 101
2	AC2	SOFTWARE	GLU A:14 , HOH A:2021 , HOH A:2023 , HOH A:2027 , HOH A:2028 , HOH A:2079	BINDING SITE FOR RESIDUE MG A 105
3	AC3	SOFTWARE	CL A:106 , HOH A:2008 , HOH A:2078	BINDING SITE FOR RESIDUE NA A 104
4	AC4	SOFTWARE	GLN A:57 , NA A:104 , HOH A:2037	BINDING SITE FOR RESIDUE CL A 106
5	AC5	SOFTWARE	SER A:15 , PHE A:16 , THR A:17 , HOH A:2075	BINDING SITE FOR RESIDUE SO4 A 102
6	AC6	SOFTWARE	PHE A:3 , VAL A:35 , TRP A:36 , VAL A:44 , ALA A:45 , ILE A:46 , GLN A:53 , HOH A:2077	BINDING SITE FOR RESIDUE C3F A 103

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:PROTEIN  Length:62
 aligned with DODEC_HALS3 | B0R5M0 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:64
                                    11        21        31        41        51        61    
           DODEC_HALS3    2 VFKKVLLTGTSEESFTAAADDAIDRAEDTLDNVVWAEVVDQGVEIGAVEERTYQTEVQVAFELD 65
               SCOP domains d4b2ha_ A: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeee...--eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  4b2h A  2 VFKKVLLTGTSEESFTAAADDAIDRAEDTLDNVVWAEVVDQGVAIGAV--RTYQTEVQVAFELD 63
                                    11        21        31        41       | -|       59    
                                                                          49 50

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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

Asymmetric Unit(hide GO term definitions)

Chain A (DODEC_HALS3 | B0R5M0)

cellular component
	GO:0005737		cytoplasm		All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829		cytosol		The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	4b2h
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

2cc8	COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
2ccb	COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
2vx9	H. SALINARUM DODECIN E45A MUTANT
4b2j	COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
4b2k	COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE
4b2l	HUMANISED MONOMERIC RADA IN COMPLEX WITH L-METHYLESTER TRYPTOPHAN
4b2m	COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

Description