2V21 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE T. THERMOPHILUS DODECIN IN COMPLEX WITH PREBOUND FMN

Authors :   B. Meissner, L. -O. Essen

Date :   31 May 07 (Deposition) - 11 Sep 07 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F  (2x)

Keywords :   Hypothetical Protein, Flavin Binding Protein, Dodecins, Coenzyme A, Flavin Dimer, Putative Storage Protein, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Meissner, E. Schleicher, S. Weber, L. -O. Essen
The Dodecin From Thermus Thermophilus, A Bifunctional Cofactor Storage Protein.
J. Biol. Chem. V. 282 33142 2007
PubMed-ID: 17855371 | Reference-DOI: 10.1074/JBC.M704951200

Molecule 1 - HYPOTHETICAL PROTEIN TTHA1431
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)GOLD
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	DODECIN

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (2x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	FMN	3	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	FMN	6	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:3 , TYR A:5 , ASP A:37 , TRP A:38 , ARG A:65 , ARG B:45 , THR B:47 , GLN B:57	BINDING SITE FOR RESIDUE FMN A 101
2	AC2	SOFTWARE	ARG A:45 , THR A:47 , GLN A:57 , LYS C:3 , TYR C:5 , ASP C:37 , TRP C:38 , ARG C:65	BINDING SITE FOR RESIDUE FMN C 101
3	AC3	SOFTWARE	VAL D:11 , ARG D:45 , THR D:47 , GLN D:57 , LYS F:3 , TYR F:5 , ASP F:37 , TRP F:38 , ARG F:65	BINDING SITE FOR RESIDUE FMN F 101
4	AC4	SOFTWARE	GLU A:19 , GLU B:19 , GLU C:19	BINDING SITE FOR RESIDUE NA A 1069
5	AC5	SOFTWARE	GLU C:68 , GLU D:19 , GLU E:19 , GLU F:19	BINDING SITE FOR RESIDUE NA F 1069

(no "SS Bond" information available for 2V21)

(no "Cis Peptide Bond" information available for 2V21)

(no "SAP(SNP)/Variant" information available for 2V21)

(no "PROSITE Motif" information available for 2V21)

(no "Exon" information available for 2V21)

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:68
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2v21a_ A: automated matches                                         SCOP domains
               CATH domains 2v21A00 A:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2v21 A  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
                                    11        21        31        41        51        61

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2v21b_ B: automated matches                                         SCOP domains
               CATH domains 2v21B00 B:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2v21 B  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
                                    11        21        31        41        51        61

Chain C from PDB  Type:PROTEIN  Length:68
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2v21c_ C: automated matches                                         SCOP domains
               CATH domains 2v21C00 C:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2v21 C  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
                                    11        21        31        41        51        61

Chain D from PDB  Type:PROTEIN  Length:68
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2v21d_ D: automated matches                                         SCOP domains
               CATH domains 2v21D00 D:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh.................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2v21 D  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
                                    11        21        31        41        51        61

Chain E from PDB  Type:PROTEIN  Length:68
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2v21e_ E: automated matches                                         SCOP domains
               CATH domains 2v21E00 E:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh.................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2v21 E  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
                                    11        21        31        41        51        61

Chain F from PDB  Type:PROTEIN  Length:68
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2v21f_ F: automated matches                                         SCOP domains
               CATH domains 2v21F00 F:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh.................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2v21 F  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
                                    11        21        31        41        51        61

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Dodecin subunit-like (56)

Superfamily: Dodecin-like (33)

Family: Dodecin-like (29)

Protein domain: automated matches (24)

Thermus thermophilus HB8 [TaxId: 300852] (6)

1a	d2v21a_	A:
1b	d2v21b_	B:
1c	d2v21c_	C:
1d	d2v21d_	D:
1e	d2v21e_	E:
1f	d2v21f_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Dodecin subunit-like (24)

Homologous Superfamily: Flavin-binding protein dodecin (24)

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. (5)

1a	2v21A00	A:2-69
1b	2v21E00	E:2-69
1c	2v21F00	F:2-69
1d	2v21B00	B:2-69
1e	2v21C00	C:2-69
1f	2v21D00	D:2-69

(no "Pfam Domain" information available for 2V21)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (DODEC_THET8 | Q5SIE3)

molecular function
	GO:0000166		nucleotide binding		Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2v21)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2v21
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	DODEC_THET8 \| Q5SIE3	:	2cz8 2deg 2ux9 2v18 2v19 2vyx

2ux9	CRYSTAL STRUCTURE OF THE T. THERMOPHILUS DODECIN R65A MUTANT
2v18	CRYSTAL STRUCTURE OF THE T. THERMOPHILUS DODECIN
2v19	CRYSTAL STRUCTURE OF THE T. THERMOPHILUS DODECIN R45A MUTANT

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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