3O03 - JenaLib

Title :   QUATERNARY COMPLEX STRUCTURE OF GLUCONATE 5-DEHYDROGENASE FROM STREPTOCOCCUS SUIS TYPE 2

Authors :   H. Peng, F. Gao, Q. Zhang, Y. Liu, G. F. Gao

Date :   18 Jul 10 (Deposition) - 15 Dec 10 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)
Biol. Unit 2: A  (2x)

Keywords :   Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Zhang, H. Peng, F. Gao, Y. Liu, H. Cheng, J. Thompson, G. F. Gao
Structural Insight Into The Catalytic Mechanism Of Gluconat 5-Dehydrogenase From Streptococcus Suis: Crystal Structures Of The Substrate-Free And Quaternary Complex Enzymes.
Protein Sci. V. 18 294 2009
PubMed-ID: 19177572 | Reference-DOI: 10.1002/PRO.32

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:150 , MET A:151 , PRO A:193 , GLY A:194 , NAP A:273 , GCO A:274 , HOH A:479	BINDING SITE FOR RESIDUE CA A 272
2	AC2	SOFTWARE	GLY A:21 , SER A:23 , TYR A:24 , GLY A:25 , ILE A:26 , ASP A:45 , ILE A:46 , LEU A:50 , CYS A:70 , ASP A:71 , VAL A:72 , ASN A:98 , ALA A:99 , GLY A:100 , ILE A:148 , CYS A:149 , TYR A:163 , LYS A:167 , THR A:198 , CA A:272 , GCO A:274 , HOH A:293 , HOH A:315 , HOH A:317 , HOH A:323 , HOH A:348 , HOH A:477	BINDING SITE FOR RESIDUE NAP A 273
3	AC3	SOFTWARE	ILE A:102 , ARG A:104 , SER A:150 , MET A:152 , ARG A:157 , VAL A:160 , TYR A:163 , CA A:272 , NAP A:273 , HOH A:478 , HOH A:479 , HOH A:482	BINDING SITE FOR RESIDUE GCO A 274

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)
	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:254
 aligned with A4VVQ2_STRSY | A4VVQ2 from UniProtKB/TrEMBL  Length:271

    Alignment length:266
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263      
         A4VVQ2_STRSY     4 QFSLDQFSLKGKIALVTGASYGIGFAIASAYAKAGATIVFNDINQELVDRGMAAYKAAGINAHGYVCDVTDEDGIQAMVAQIESEVGIIDILVNNAGIIRRVPMIEMTAAQFRQVIDIDLNAPFIVSKAVIPSMIKKGHGKIINICSMMSELGRETVSAYAAAKGGLKMLTKNIASEYGEANIQCNGIGPGYIATPQTAPLRELQKDGSRHPFDQFIIAKTPAARWGEAEDLMGPAVFLASDASNFVNGHILYVDGGILAYIGKQP 269
               SCOP domains d3o03a_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------adh_short-3o03A01 A:15-182                                                                                                                                              --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee........------------hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o03 A   4 QFSLDQFSLKGKIALVTGASYGIGFAIASAYAKAGATIVFNDINQELVDRGMAAYKAAGINAHGYVCDVTDEDGIQAMVAQIESEVGIIDILVNNAGIIRRVPMIEMTAAQFRQVIDIDLNAPFIVSKAVIPSMIKKGHGKIINICSMMSELGRETVSAYAAAKGGLKMLTKNIASEYGEANIQCNGIGPGYIATPQT------------HPFDQFIIAKTPAARWGEAEDLMGPAVFLASDASNFVNGHILYVDGGILAYIGKQP 269
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       | -         -|      223       233       243       253       263      
                                                                                                                                                                                                                               201          214

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 (1, 1)

CATH Domains (0, 0 ; only for superseded entry 3CXT: 1,1)

Pfam Domains (1, 1)

Gene Ontology (4, 4)

Asymmetric Unit(hide GO term definitions)

Chain A (A4VVQ2_STRSY | A4VVQ2)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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	Sites
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		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3o03)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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