4HP8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PUTATIVE 2-DEOXY-D-GLUCONATE 3-DEHYDROGENASE FROM AGROBACTERIUM TUMEFACIENS (TARGET EFI-506435) WITH BOUND NADP

Authors :   M. W. Vetting, J. T. Bouvier, F. Groninger-Poe, L. L. Morisco, S. R. Wass S. Sojitra, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Function Init (Efi)

Date :   23 Oct 12 (Deposition) - 07 Nov 12 (Release) - 07 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Enzyme Function Initiative, Efi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Vetting, J. T. Bouvier, F. Groninger-Poe, L. L. Morisco, S. R. Wasserman, S. Sojitra, H. J. Imker, J. A. Gerlt, S. C. Almo
Crystal Structure Of A Putative 2-Deoxy-D-Gluconate 3-Dehydrogenase From Agrobacterium Tumefaciens (Target Efi-506435) With Bound Nadp
To Be Published
PubMed: search

Molecule 1 - 2-DEOXY-D-GLUCONATE 3-DEHYDROGENASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	KDUD, ATU3141
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	176299
	Strain	:	C58 / ATCC 33970

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:16 , ASN A:18 , THR A:19 , GLY A:20 , LEU A:21 , ARG A:41 , ARG A:42 , ILE A:63 , ASP A:64 , PHE A:65 , ALA A:66 , ASN A:86 , ALA A:87 , GLY A:88 , ILE A:89 , ILE A:137 , ALA A:138 , TYR A:152 , LYS A:156 , PRO A:182 , GLY A:183 , TYR A:184 , ILE A:185 , THR A:187 , ASN A:188 , ASN A:189 , THR A:190 , HOH A:403 , HOH A:434 , HOH A:457 , HOH A:471 , HOH A:491 , HOH A:511 , HOH A:512 , HOH A:520 , HOH A:564 , HOH A:578 , HOH A:676	BINDING SITE FOR RESIDUE NAP A 301
2	AC2	SOFTWARE	ILE A:90 , ARG A:92 , TYR A:184 , HOH A:437 , HOH A:443	BINDING SITE FOR RESIDUE ACT A 302
3	AC3	SOFTWARE	GLY B:16 , ASN B:18 , THR B:19 , GLY B:20 , LEU B:21 , ARG B:41 , ARG B:42 , ILE B:63 , ASP B:64 , PHE B:65 , ALA B:66 , ASN B:86 , ALA B:87 , GLY B:88 , ILE B:89 , ILE B:137 , ALA B:138 , TYR B:152 , LYS B:156 , PRO B:182 , GLY B:183 , ILE B:185 , THR B:187 , ASN B:189 , THR B:190 , HOH B:404 , HOH B:444 , HOH B:447 , HOH B:449 , HOH B:450 , HOH B:493 , HOH B:498 , HOH B:545 , HOH B:551 , HOH B:555 , HOH B:580 , HOH B:586 , HOH B:611 , HOH B:672 , HOH B:673	BINDING SITE FOR RESIDUE NAP B 301

(no "SS Bond" information available for 4HP8)

(no "Cis Peptide Bond" information available for 4HP8)

(no "SAP(SNP)/Variant" information available for 4HP8)

(no "PROSITE Motif" information available for 4HP8)

(no "Exon" information available for 4HP8)

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:245
                                                                                                                                                                                                                                                                                     
               SCOP domains d4hp8a_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhh...eeeee...................eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hp8 A   3 NPFSLEGRKALVTGANTGLGQAIAVGLAAAGAEVVCAARRAPDETLDIIAKDGGNASALLIDFADPLAAKDSFTDAGFDILVNNAGIIRRADSVEFSELDWDEVMDVNLKALFFTTQAFAKELLAKGRSGKVVNIASLLSFQGGIRVPSYTAAKHGVAGLTKLLANEWAAKGINVNAIAPGYIETNNTEALRADAARNKAILERIPAGRWGHSEDIAGAAVFLSSAAADYVHGAILNVDGGWLAR 247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains d4hp8b_ B: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee....hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhh...eeeee...................eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hp8 B   2 KNPFSLEGRKALVTGANTGLGQAIAVGLAAAGAEVVCAARRAPDETLDIIAKDGGNASALLIDFADPLAAKDSFTDAGFDILVNNAGIIRRADSVEFSELDWDEVMDVNLKALFFTTQAFAKELLAKGRSGKVVNIASLLSFQGGIRVPSYTAAKHGVAGLTKLLANEWAAKGINVNAIAPGYIETNNTEALRADAARNKAILERIPAGRWGHSEDIAGAAVFLSSAAADYVHGAILNVDGGWLAR 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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

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Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Agrobacterium tumefaciens [TaxId: 176299] (2)

1a	d4hp8a_	A:
1b	d4hp8b_	B:

(no "CATH Domain" information available for 4HP8)

(no "Pfam Domain" information available for 4HP8)

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