3NB8 - JenaLib

Title :   CRYSTAL STRUCTURE OF OXIDIZED H88Q SYNECHOCYSTIS SP. PCYA

Authors :   D. D. Gae

Date :   03 Jun 10 (Deposition) - 06 Oct 10 (Release) - 16 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha-Beta-Alpha Sandwich, Radical Chemistry, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. C. Kohler, D. D. Gae, M. A. Richley, S. Stoll, A. Gunn, S. Lim, S. S. Martin, T. I. Doukov, R. D. Britt, J. B. Ames, J. C. Lagarias, A. J. Fisher
Structural Basis For Hydration Dynamics In Radical Stabilization Of Bilin Reductase Mutants.
Biochemistry V. 49 6206 2010
PubMed-ID: 20557110 | Reference-DOI: 10.1021/BI100728Q

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 15)

Sites (15, 15)

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:185 , ARG A:224 , GLU A:227	BINDING SITE FOR RESIDUE EDO A 401
02	AC2	SOFTWARE	MET A:20 , GLU A:173 , GLU A:174 , EDO A:410	BINDING SITE FOR RESIDUE EDO A 402
03	AC3	SOFTWARE	GLY A:47 , TYR A:48 , GLU A:61 , ASN A:62 , EDO A:411 , HOH A:1236 , HOH A:1237 , HOH A:1374	BINDING SITE FOR RESIDUE EDO A 403
04	AC4	SOFTWARE	ALA A:132 , TYR A:133 , GLN A:190 , HOH A:1117 , HOH A:1249 , HOH A:1261	BINDING SITE FOR RESIDUE EDO A 404
05	AC5	SOFTWARE	LEU A:151 , CYS A:162 , PHE A:164 , HOH A:1040 , HOH A:1048 , HOH A:1080	BINDING SITE FOR RESIDUE EDO A 405
06	AC6	SOFTWARE	ASN A:169 , VAL A:170 , THR A:171 , HOH A:1089 , HOH A:1139	BINDING SITE FOR RESIDUE EDO A 406
07	AC7	SOFTWARE	SER A:31 , LEU A:184 , GLN A:185 , CYS A:188 , LYS A:221 , HOH A:1043 , HOH A:1055 , HOH A:1112 , HOH A:1292	BINDING SITE FOR RESIDUE EDO A 407
08	AC8	SOFTWARE	GLN A:124 , GLN A:201 , GLU A:204 , HOH A:1073 , HOH A:1085 , HOH A:1182 , HOH A:1263	BINDING SITE FOR RESIDUE EDO A 408
09	AC9	SOFTWARE	ASN A:10 , SER A:12 , TYR A:48 , GLU A:61	BINDING SITE FOR RESIDUE EDO A 409
10	BC1	SOFTWARE	MET A:20 , GLN A:23 , GLU A:173 , GLU A:174 , VAL A:177 , EDO A:402 , HOH A:1062	BINDING SITE FOR RESIDUE EDO A 410
11	BC2	SOFTWARE	ASP A:45 , LEU A:46 , GLY A:47 , GLU A:54 , EDO A:403	BINDING SITE FOR RESIDUE EDO A 411
12	BC3	SOFTWARE	THR A:171 , ARG A:175 , HOH A:1074	BINDING SITE FOR RESIDUE EDO A 412
13	BC4	SOFTWARE	ASN A:18 , PRO A:19 , GLU A:173 , HOH A:1024 , HOH A:1046 , HOH A:1138 , HOH A:1275	BINDING SITE FOR RESIDUE EDO A 414
14	BC5	SOFTWARE	GLN A:41 , LEU A:42 , GLU A:44 , HOH A:1134	BINDING SITE FOR RESIDUE EDO A 415
15	BC6	SOFTWARE	SER A:34 , GLU A:76 , ILE A:86 , GLN A:88 , VAL A:90 , GLY A:103 , CYS A:104 , ASP A:105 , VAL A:107 , SER A:114 , ALA A:115 , ARG A:149 , PHE A:158 , PHE A:164 , ILE A:192 , GLN A:216 , LYS A:221 , THR A:222 , VAL A:225 , PHE A:244 , HOH A:1042 , HOH A:1067 , HOH A:1146 , HOH A:1151 , HOH A:1171 , HOH A:1231 , HOH A:1400	BINDING SITE FOR RESIDUE BLA A 249

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/Biological 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:242
 aligned with PCYA_SYNY3 | Q55891 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:242
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245  
           PCYA_SYNY3     6 LSLTNSSLMPTLNPMIQQLALAIAASWQSLPLKPYQLPEDLGYVEGRLEGEKLVIENRCYQTPQFRKMHLELAKVGKGLDILHCVMFPEPLYGLPLFGCDIVAGPGGVSAAIADLSPTQSDRQLPAAYQKSLAELGQPEFEQQRELPPWGEIFSEYCLFIRPSNVTEEERFVQRVVDFLQIHCHQSIVAEPLSEAQTLEHRQGQIHYCQQQQKNDKTRRVLEKAFGEAWAERYMSQVLFDVI 247
               SCOP domains d3nb8a_ A: Ferredoxin-dependent bilin reductase                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------Fe_bilin_red-3nb8A01 A:25-245                                                                                                                                                                                                -- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhh....ee..hhhhh.eeee......eeeeeeeee...eeeeeeeeeee...eeeeeeeeee.hhhh..eeeeeeeee..eeeeeeeeee........hhhhhhhhhh............hhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nb8 A   6 LSLTNSSLMPTLNPMIQQLALAIAASWQSLPLKPYQLPEDLGYVEGRLEGEKLVIENRCYQTPQFRKMHLELAKVGKGLDILQCVMFPEPLYGLPLFGCDIVAGPGGVSAAIADLSPTQSDRQLPAAYQKSLAELGQPEFEQQRELPPWGEIFSEYCLFIRPSNVTEEERFVQRVVDFLQIHCHQSIVAEPLSEAQTLEHRQGQIHYCQQQQKNDKTRRVLEKAFGEAWAERYMSQVLFDVI 247
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245

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)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PCYA_SYNY3 | Q55891)

molecular function
	GO:0050897	cobalt ion binding	Interacting selectively and non-covalently with a cobalt (Co) ion.
	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.
	GO:0016636	oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces an iron-sulfur protein.
	GO:0050620	phycocyanobilin:ferredoxin oxidoreductase activity	Catalysis of the reaction: (3Z)-phycocyanobilin + oxidized ferredoxin = biliverdin IXa + reduced ferredoxin.
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.
	GO:0010024	phytochromobilin biosynthetic process	The chemical reactions and pathways resulting in the formation of phytochromobilin, which involves the oxidative cleavage of heme by a heme oxygenase(HO) to form biliverdin IX alpha.

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	3nb8
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