1Y89 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DEVB PROTEIN

Authors :   K. Lazarski, M. Cymborowski, M. Chruszcz, H. Zheng, R. Zhang, L. Lezond A. Joachimiak, W. Minor, Midwest Center For Structural Genomics

Date :   10 Dec 04 (Deposition) - 25 Jan 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   K. Lazarski, M. Cymborowski, M. Chruszcz, H. Zheng, R. Zhang, L. Lezondra, A. Joachimiak, W. Minor
Crystal Structure Of Devb Protein
To Be Published
PubMed: search

Molecule 1 - DEVB PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961
	Organism Taxid	:	243277
	Strain	:	O1 BIOVAR ELTOR STR. N16961

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 20)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
3	PE5	2	Ligand/Ion	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PO4	6	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:70 , HIS A:144 , ARG A:173 , PO4 A:241 , HOH A:1087 , HOH A:1366 , HOH A:1383 , HOH A:1452	BINDING SITE FOR RESIDUE PO4 A 239
02	AC2	SOFTWARE	SER A:39 , THR A:40 , LYS A:196 , HOH A:1010 , HOH A:1113 , HOH A:1264 , HOH A:1310 , HOH A:1380 , HOH A:1414 , HOH A:1575	BINDING SITE FOR RESIDUE PO4 A 240
03	AC3	SOFTWARE	GLY A:140 , ALA A:141 , ASP A:142 , HIS A:144 , PO4 A:239 , HOH A:1188 , HOH A:1313 , HOH A:1387 , HOH A:1541	BINDING SITE FOR RESIDUE PO4 A 241
04	AC4	SOFTWARE	ARG B:70 , HIS B:144 , ARG B:173 , PO4 B:241 , HOH B:1111 , HOH B:1173 , HOH B:1205 , HOH B:1518	BINDING SITE FOR RESIDUE PO4 B 239
05	AC5	SOFTWARE	SER B:39 , THR B:40 , LYS B:196 , HOH B:1170 , HOH B:1200 , HOH B:1292	BINDING SITE FOR RESIDUE PO4 B 240
06	AC6	SOFTWARE	GLY B:140 , ALA B:141 , ASP B:142 , HIS B:144 , PO4 B:239 , HOH B:1173 , HOH B:1497	BINDING SITE FOR RESIDUE PO4 B 241
07	AC7	SOFTWARE	HIS A:4 , ILE A:203 , HIS A:204 , TRP A:227 , ILE A:237 , HIS B:4 , ILE B:203 , HIS B:204 , TRP B:227 , ILE B:237 , PE5 B:243 , PEG B:244 , HOH B:1464 , HOH B:1562	BINDING SITE FOR RESIDUE 2PE B 242
08	AC8	SOFTWARE	ILE A:237 , HIS B:204 , THR B:205 , THR B:206 , PRO B:207 , 2PE B:242	BINDING SITE FOR RESIDUE PE5 B 243
09	AC9	SOFTWARE	ASP A:20 , ALA A:23 , TYR A:24 , ARG A:186	BINDING SITE FOR RESIDUE PE5 A 242
10	BC1	SOFTWARE	THR A:205 , THR A:206 , PRO A:207 , HOH A:1423 , ILE B:237 , ALA B:238 , 2PE B:242 , HOH B:1505	BINDING SITE FOR RESIDUE PEG B 244

(no "SS Bond" information available for 1Y89)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:51	-	Pro A:52
2	Gln B:51	-	Pro B:52

(no "SAP(SNP)/Variant" information available for 1Y89)

(no "PROSITE Motif" information available for 1Y89)

(no "Exon" information available for 1Y89)

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:238
 aligned with Q9KL51_VIBCH | Q9KL51 from UniProtKB/TrEMBL  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q9KL51_VIBCH     1 MINHKIFPTADAVVKSLADDMLAYSQQGQPVHISLSGGSTPKMLFKLLASQPYANDIQWKNLHFWWGDERCVAPDDAESNYGEANALLFSKINMPAQNIHRILGENEPQAEAERFAQAMAHVIPTENGTPVFDWILLGVGADGHTASLFPGQTDYADANLSVVASHPESGQLRVSKTAKVLQAAKRISYLVLGAGKAEIVEQIHTTPAEQLPYPAAKIHSTSGVTEWYLDSDAAAKIA 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -1y89A00 A:2-238  [code=3.40.50.1360, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh..hhhhhhhhh.eeeee.eee........hhhhhhhhhhhhhh..hhhhh.......hhhhhhhhhhhhhhhhh.ee..ee...eeee.......................eeeee......eeeeehhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhh.hhhhhh.....eeeeeeehhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y89 A   1 mINHKIFPTADAVVKSLADDmLAYSQQGQPVHISLSGGSTPKmLFKLLASQPYANDIQWKNLHFWWGDERCVAPDDAESNYGEANALLFSKINmPAQNIHRILGENEPQAEAERFAQAmAHVIPTENGTPVFDWILLGVGADGHTASLFPGQTDYADANLSVVASHPESGQLRVSKTAKVLQAAKRISYLVLGAGKAEIVEQIHTTPAEQLPYPAAKIHSTSGVTEWYLDSDAAAKIA 238
                            |       10        20|       30        40  |     50        60        70        80        90   |   100       110       120       130       140       150       160       170       180       190       200       210       220       230        
                            |                  21-MSE                43-MSE                                             94-MSE                  119-MSE                                                                                                                   
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with Q9KL51_VIBCH | Q9KL51 from UniProtKB/TrEMBL  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q9KL51_VIBCH     1 MINHKIFPTADAVVKSLADDMLAYSQQGQPVHISLSGGSTPKMLFKLLASQPYANDIQWKNLHFWWGDERCVAPDDAESNYGEANALLFSKINMPAQNIHRILGENEPQAEAERFAQAMAHVIPTENGTPVFDWILLGVGADGHTASLFPGQTDYADANLSVVASHPESGQLRVSKTAKVLQAAKRISYLVLGAGKAEIVEQIHTTPAEQLPYPAAKIHSTSGVTEWYLDSDAAAKIA 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -1y89B00 B:2-238  [code=3.40.50.1360, no name defined]                                                                                                                                                                                         CATH domains
           Pfam domains (1) --------Glucosamine_iso-1y89B01 B:9-205                                                                                                                                                                      --------------------------------- Pfam domains (1)
           Pfam domains (2) --------Glucosamine_iso-1y89B02 B:9-205                                                                                                                                                                      --------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh..hhhhhhhhh.eeeee.eee........hhhhhhhhhhhhhh..hhhhh.......hhhhhhhhhhhhhhhhh.ee..ee...eeee.......................eeeee......eeeeehhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhh.hhhhhh.....eeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y89 B   1 mINHKIFPTADAVVKSLADDmLAYSQQGQPVHISLSGGSTPKmLFKLLASQPYANDIQWKNLHFWWGDERCVAPDDAESNYGEANALLFSKINmPAQNIHRILGENEPQAEAERFAQAmAHVIPTENGTPVFDWILLGVGADGHTASLFPGQTDYADANLSVVASHPESGQLRVSKTAKVLQAAKRISYLVLGAGKAEIVEQIHTTPAEQLPYPAAKIHSTSGVTEWYLDSDAAAKIA 238
                            |       10        20|       30        40  |     50        60        70        80        90   |   100       110       120       130       140       150       160       170       180       190       200       210       220       230        
                            1-MSE              21-MSE                43-MSE                                             94-MSE                  119-MSE

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 '\|'

(no "SCOP Domain" information available for 1Y89)

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: [code=3.40.50.1360, no name defined] (40)

N16961 (Vibrio cholerae o1 biovar eltor str) (1)

1a	1y89A00	A:2-238
1b	1y89B00	B:2-238

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ISOCOT_Fold (53)

Family: Glucosamine_iso (12)

Vibrio cholerae (1)

1a	Glucosamine_iso-1y89B01	B:9-205
1b	Glucosamine_iso-1y89B02	B:9-205

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q9KL51_VIBCH | Q9KL51)

molecular function
	GO:0017057	6-phosphogluconolactonase activity	Catalysis of the reaction: 6-O-phosphono-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate + H(+).
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.
	GO:0006098	pentose-phosphate shunt	The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gln A:51 - Pro A:52	[ RasMol ]
		Gln B:51 - Pro B:52	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (5, 20)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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