1Y7P - JenaLib

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Title :   1.9 A CRYSTAL STRUCTURE OF A PROTEIN OF UNKNOWN FUNCTION AF1403 FROM ARCHAEOGLOBUS FULGIDUS, PROBABLE METABOLIC REGULATOR

Authors :   R. Zhang, T. Skarina, A. Savchenko, A. Edwards, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   09 Dec 04 (Deposition) - 01 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B  (2x)
Biol. Unit 3: A (2x),B (2x),C (2x)
Biol. Unit 4: A (1x),B (1x),C (1x)

Keywords :   Structural Genomics, Protein Structure Initiative, Psi, Archaeoglobus Fulgidus, Alpha-Beta-Alpha Sandwich, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Zhang, T. Skarina, A. Savchenko, A. Edwards, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
1. 9A Crystal Structure Of A Hypothetical Protein Af1403 From Archaeoglobus Fulgidus
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN AF1403
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AF1403
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Strain	:	VC-16-DSM4304-ATCC49558

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (2x)	:		B
Biological Unit 3 (2x)	:	A (2x)	B (2x)	C (2x)
Biological Unit 4 (1x)	:	A (1x)	B (1x)	C (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	RIP	3	Ligand/Ion	RIBOSE(PYRANOSE FORM)
2	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	RIP	2	Ligand/Ion	RIBOSE(PYRANOSE FORM)
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	RIP	2	Ligand/Ion	RIBOSE(PYRANOSE FORM)
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	RIP	-1	Ligand/Ion	RIBOSE(PYRANOSE FORM)
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	RIP	1	Ligand/Ion	RIBOSE(PYRANOSE FORM)
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:87 , ILE A:89 , ASP A:121 , THR A:122 , LEU A:141 , PHE C:84 , ARG C:87 , SER C:119 , ASP C:121 , ARG C:143 , HOH C:403	BINDING SITE FOR RESIDUE RIP C 4181
2	AC2	SOFTWARE	PHE A:84 , ARG A:87 , SER A:119 , ASP A:121 , ARG A:143 , HOH A:402 , HOH A:466 , ARG C:87 , ILE C:89 , ASP C:121 , LEU C:141	BINDING SITE FOR RESIDUE RIP A 4182
3	AC3	SOFTWARE	PHE B:84 , ARG B:87 , SER B:119 , ASP B:121 , THR B:122 , LEU B:141 , ARG B:143 , HOH B:310 , HOH B:317	BINDING SITE FOR RESIDUE RIP B 4183
4	AC4	SOFTWARE	MET A:201 , HIS A:202 , SER A:204 , ALA A:207 , PHE A:209 , HOH A:420	BINDING SITE FOR RESIDUE ZN A 301
5	AC5	SOFTWARE	MET C:201 , HIS C:202 , SER C:204 , ALA C:207 , PHE C:209	BINDING SITE FOR RESIDUE ZN C 302
6	AC6	SOFTWARE	MET B:201 , HIS B:202 , SER B:204 , ALA B:207 , PHE B:209	BINDING SITE FOR RESIDUE ZN B 303

(no "SS Bond" information available for 1Y7P)

(no "Cis Peptide Bond" information available for 1Y7P)

(no "SAP(SNP)/Variant" information available for 1Y7P)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	Y1403_ARCFU	4-79	2	A:4-79 B:4-79

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	Y1403_ARCFU	4-79	1	A:4-79 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	Y1403_ARCFU	4-79	2	- B:4-79

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	Y1403_ARCFU	4-79	4	A:4-79 B:4-79

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	Y1403_ARCFU	4-79	2	A:4-79 B:4-79

(no "Exon" information available for 1Y7P)

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:212
 aligned with Y1403_ARCFU | O28869 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
          Y1403_ARCFU     2 LRGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEIEGGDFEKILERVKTFDYIIEIEEEESFERVFGKRVIILGGGALVSQVAIGAISEADRHNLRGERISVDTMPVVGEEEIAEAVKAVSRLHRAEVLVLAGGIMGGKITEEVKKLRKSGIRVISLSMFGSVPDVADVVISDPVMAGTLAVMHISEKAKFDLDRVKGR 217
               SCOP domains d1y7pa2 A:2-78 Hypothet    ical protein AF1403, N-terminal domain            d1y7pa1 A:79-217 Hypothetical protein AF1403, C-terminal domain                                                                             SCOP domains
               CATH domains 1y7pA01 A:2-78  [code=3    .30.70.260, no name defined]                      1y7pA02 A:79-217 Hypothetical protein af1403; domain 2                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhh.----.eeeeeeee........eeeeeeee...hhhhhhhhhhh...eeeeeee.hhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhh.eeeee....hhhhhh.eee.hhhhhhhhhhhhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --ACT  PDB: A:4-79 UniProt: 4-79                                              ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y7p A   2 LRGLRIIAENKIGVLRDLTTIIA----NITFAQTFLIKHGEHEGKALIYFEIEGGDFEKILERVKTFDYIIEIEEEESFERVFGKRVIILGGGALVSQVAIGAISEADRHNLRGERISVDTMPVVGEEEIAEAVKAVSRLHRAEVLVLAGGIMGGKITEEVKKLRKSGIRVISLSMFGSVPDVADVVISDPVMAGTLAVMHISEKAKFDLDRVKGR 217
                                    11        21  |    |31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
                                                 24   29

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with Y1403_ARCFU | O28869 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:217
                              1                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       
          Y1403_ARCFU     - --MLRGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEIEGGDFEKILERVKTFDYIIEIEEEESFERVFGKRVIILGGGALVSQVAIGAISEADRHNLRGERISVDTMPVVGEEEIAEAVKAVSRLHRAEVLVLAGGIMGGKITEEVKKLRKSGIRVISLSMFGSVPDVADVVISDPVMAGTLAVMHISEKAKFDLDRVK 215
               SCOP domains d1y7pb2 B:-1-78 Hypothetical protein AF1403, N-terminal domain                  d1y7pb1 B:79-215 Hypothetical protein AF1403, C-terminal domain                                                                           SCOP domains
               CATH domains 1y7pB01 B:-1-78  [code=3.30.70.260, no name defined]                            1y7pB02 B:79-215 Hypothetical protein af1403; domain 2                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhhh..eeeeeeeee..hhhhh..eeeeeeee..hhhhhhhhhh....eeeeeee.hhhhhhheeeeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhh..eeeee....hhhhhh.eee.hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----ACT  PDB: B:4-79 UniProt: 4-79                                              ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y7p B  -1 GHMLRGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEIEGGDFEKILERVKTFDYIIEIEEEESFERVFGKRVIILGGGALVSQVAIGAISEADRHNLRGERISVDTMPVVGEEEIAEAVKAVSRLHRAEVLVLAGGIMGGKITEEVKKLRKSGIRVISLSMFGSVPDVADVVISDPVMAGTLAVMHISEKAKFDLDRVK 215
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain C from PDB  Type:PROTEIN  Length:206
 aligned with Y1403_ARCFU | O28869 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:217
                                                                                                                                                                                                                                                219  
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    |  
          Y1403_ARCFU     5 LRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEIEGGDFEKILERVKTFDYIIEIEEEESFERVFGKRVIILGGGALVSQVAIGAISEADRHNLRGERISVDTMPVVGEEEIAEAVKAVSRLHRAEVLVLAGGIMGGKITEEVKKLRKSGIRVISLSMFGSVPDVADVVISDPVMAGTLAVMHISEKAKFDLDRVKGRRI--   -
               SCOP domains d1y7pc2 C:5-78 Hypothe   tical protein AF1403, N        -terminal domain  d1y7pc1 C:79-221 Hypothetical protein AF1403, C-terminal domain                                                                                 SCOP domains
               CATH domains 1y7pC01 C:5-84  [code=   3.30.70.260, no name de        fined]                  1y7pC02 C:85-221 Hypothetical protein af1403; domain 2                                                                                    CATH domains
           Pfam domains (1) ACT-1y7pC01 C:5-69                                               -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ACT-1y7pC02 C:5-69                                               -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ACT-1y7pC03 C:5-69                                               -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .eeee.....hhhhhhhhhhhh---...eeeee.........eeeee.--------hhhhhhh...eee.....hhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhh..eeeee....hhhhhh.eee.hhhhhhhhhhhhhh.....hhhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ACT  PDB: - UniProt: 4-79                                                  ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y7p C   5 LRIIAENKIGVLRDLTTIIAEE---ITFAQTFLIKHGEHEGKALIYFE--------ILERVKTFDYIIEIEEEESFERVFGKRVIILGGGALVSQVAIGAISEADRHNLRGERISVDTMPVVGEEEIAEAVKAVSRLHRAEVLVLAGGIMGGKITEEVKKLRKSGIRVISLSMFGSVPDVADVVISDPVMAGTLAVMHISEKAKFDLDRVKGRRIGK 221
                                    14        24 |   |  34        44       | -      | 64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
                                                26  30                    52       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: Ferredoxin-like (1795)

Superfamily: ACT-like (63)

Family: AF1403 N-terminal domain-like (1)

Protein domain: Hypothetical protein AF1403, N-terminal domain (1)

Archaeoglobus fulgidus [TaxId: 2234] (1)

1a	d1y7pa2	A:2-78
1b	d1y7pb2	B:-1-78
1c	d1y7pc2	C:5-78

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

Fold: Flavodoxin-like (1057)

Superfamily: CheY-like (258)

Family: AF1403 C-terminal domain-like (1)

Protein domain: Hypothetical protein AF1403, C-terminal domain (1)

Archaeoglobus fulgidus [TaxId: 2234] (1)

2a	d1y7pa1	A:79-217
2b	d1y7pb1	B:79-215
2c	d1y7pc1	C:79-221

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ACT (34)

Family: ACT (19)

Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (1)

1a	ACT-1y7pC01	C:5-69
1b	ACT-1y7pC02	C:5-69
1c	ACT-1y7pC03	C:5-69

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Y1403_ARCFU | O28869)

molecular function
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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