1VIM - JenaLib

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Title :   CRYSTAL STRUCTURE OF AN HYPOTHETICAL PROTEIN

Authors :   Structural Genomix

Date :   01 Dec 03 (Deposition) - 30 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.36

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622 | Reference-DOI: 10.1002/PROT.20541

Molecule 1 - HYPOTHETICAL PROTEIN AF1796
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	AF1796
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	FMT	5	Ligand/Ion	FORMIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:72 , ARG A:73 , ILE A:74 , ALA C:180 , VAL C:181 , LEU C:182 , HOH C:194	BINDING SITE FOR RESIDUE FMT C 188
2	AC2	SOFTWARE	ALA A:180 , VAL A:181 , LEU A:182 , HOH A:191 , PRO C:72 , ARG C:73 , ILE C:74	BINDING SITE FOR RESIDUE FMT A 188
3	AC3	SOFTWARE	PRO B:72 , ARG B:73 , ILE B:74 , ALA D:180 , VAL D:181 , LEU D:182 , HOH D:199	BINDING SITE FOR RESIDUE FMT D 188
4	AC4	SOFTWARE	ALA B:180 , VAL B:181 , LEU B:182 , HOH B:201 , PRO D:72 , ARG D:73 , ILE D:74	BINDING SITE FOR RESIDUE FMT B 188
5	AC5	SOFTWARE	ARG B:35 , LYS D:128 , LYS D:130 , MET D:131 , LYS D:132	BINDING SITE FOR RESIDUE FMT D 189

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

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

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIS	PS51464	SIS domain profile.	Y1796_ARCFU	27-170	4	A:27-170 B:27-170 C:27-170 D:27-170

(no "Exon" information available for 1VIM)

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:192
 aligned with Y1796_ARCFU | O28478 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:192
                                  1                                                                                                                                                                                   183   
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174        |-  
          Y1796_ARCFU     - ------MLRFLEVVSEHIKNLRNHIDLETVGEMIKLIDSARSIFVIGAGRSGYIAKAFAMRLMHLGYTVYVVGETVTPRITDQDVLVAISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLAKMADVVMVVKGKMKQERDEILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEARHAVLE---   -
               SCOP domains d1vima_ A: Hypothetical protein AF1796                                                                                                                                                           SCOP domains
               CATH domains 1vimA00 A:-5-186 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh...eee.............eeeee.....hhhhhhhhhhhhhhh.eeeeee....hhhhhhh.eeee........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------SIS  PDB: A:27-170 UniProt: 27-170                                                                                                              ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vim A  -5 HGGHMSLLRFLEVVSEHIKNLRNHIDLETVGEMIKLIDSARSIFVIGAGRSGYIAKAFAMRLMHLGYTVYVVGETVTPRITDQDVLVGISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLAKMADVVMVVKGKMKQERDEILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEARHAVLEEGG 186
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with Y1796_ARCFU | O28478 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:188
                               1                                                                                                                                                                                   183  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177     |  
          Y1796_ARCFU     - ---MLRFLEVVSEHIKNLRNHIDLETVGEMIKLIDSARSIFVIGAGRSGYIAKAFAMRLMHLGYTVYVVGETVTPRITDQDVLVAISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLAKMADVVMVVKGKMKQERDEILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEARHAVLE--   -
               SCOP domains d1vimb_ B: Hypothetical protein AF1796                                                                                                                                                       SCOP domains
               CATH domains 1vimB00 B:-2-185 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhh...eee.............eeeee.....hhhhhhhhhhhhhhh.eeeeee....hhhhhhh.eeee........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------SIS  PDB: B:27-170 UniProt: 27-170                                                                                                              --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vim B  -2 HMSLLRFLEVVSEHIKNLRNHIDLETVGEMIKLIDSARSIFVIGAGRSGYIAKAFAMRLMHLGYTVYVVGETVTPRITDQDVLVGISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLAKMADVVMVVKGKMKQERDEILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEARHAVLEEG 185
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177

Chain C from PDB  Type:PROTEIN  Length:190
 aligned with Y1796_ARCFU | O28478 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:190
                                 1                                                                                                                                                                                   183  
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       | -
          Y1796_ARCFU     - -----MLRFLEVVSEHIKNLRNHIDLETVGEMIKLIDSARSIFVIGAGRSGYIAKAFAMRLMHLGYTVYVVGETVTPRITDQDVLVAISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLAKMADVVMVVKGKMKQERDEILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEARHAVLE--   -
               SCOP domains d1vimc_ C: Hypothetical protein AF1796                                                                                                                                                         SCOP domains
               CATH domains 1vimC00 C:-4-185 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh..eee.............eeeee.....hhhhhhhhhhhhhhh.eeeeee....hhhhhhh.eeee........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------SIS  PDB: C:27-170 UniProt: 27-170                                                                                                              --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vim C  -4 GGHMSLLRFLEVVSEHIKNLRNHIDLETVGEMIKLIDSARSIFVIGAGRSGYIAKAFAMRLMHLGYTVYVVGETVTPRITDQDVLVGISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLAKMADVVMVVKGKMKQERDEILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEARHAVLEEG 185
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain D from PDB  Type:PROTEIN  Length:190
 aligned with Y1796_ARCFU | O28478 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:190
                                 1                                                                                                                                                                                   183  
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       | -
          Y1796_ARCFU     - -----MLRFLEVVSEHIKNLRNHIDLETVGEMIKLIDSARSIFVIGAGRSGYIAKAFAMRLMHLGYTVYVVGETVTPRITDQDVLVAISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLAKMADVVMVVKGKMKQERDEILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEARHAVLE--   -
               SCOP domains d1vimd_ D: Hypothetical protein AF1796                                                                                                                                                         SCOP domains
               CATH domains 1vimD00 D:-4-185 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                          CATH domains
           Pfam domains (1) ----------------------------------SIS-1vimD01 D:30-161                                                                                                                ------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------SIS-1vimD02 D:30-161                                                                                                                ------------------------ Pfam domains (2)
           Pfam domains (3) ----------------------------------SIS-1vimD03 D:30-161                                                                                                                ------------------------ Pfam domains (3)
           Pfam domains (4) ----------------------------------SIS-1vimD04 D:30-161                                                                                                                ------------------------ Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhh...eee.............eeeee.....hhhhhhhhhhhhhhh.eeeeee....hhhhhhh.eeee........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------SIS  PDB: D:27-170 UniProt: 27-170                                                                                                              --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vim D  -4 GGHMSLLRFLEVVSEHIKNLRNHIDLETVGEMIKLIDSARSIFVIGAGRSGYIAKAFAMRLMHLGYTVYVVGETVTPRITDQDVLVGISGSGETTSVVNISKKAKDIGSKLVAVTGKRDSSLAKMADVVMVVKGKMKQERDEILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEARHAVLEEG 185
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: SIS domain (85)

Superfamily: SIS domain (85)

Family: mono-SIS domain (10)

Protein domain: Hypothetical protein AF1796 (1)

Archaeoglobus fulgidus [TaxId: 2234] (1)

1a	d1vima_	A:
1b	d1vimb_	B:
1c	d1vimc_	C:
1d	d1vimd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Glucose-6-phosphate isomerase like protein; domain 1 (105)

Archaeoglobus fulgidus. Organism_taxid: 2234. (1)

1a	1vimA00	A:-5-186
1b	1vimC00	C:-4-185
1c	1vimD00	D:-4-185
1d	1vimB00	B:-2-185

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SIS (53)

Family: SIS (23)

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

1a	SIS-1vimD01	D:30-161
1b	SIS-1vimD02	D:30-161
1c	SIS-1vimD03	D:30-161
1d	SIS-1vimD04	D:30-161

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Y1796_ARCFU | O28478)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vim)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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