3IEB - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 3-KETO-L-GULONATE-6-PHOSPHATE DECARBOXYLASE FROM VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961

Authors :   B. Nocek, N. Maltseva, J. Osipiuk, J. Stam, W. Anderson, A. Joachimiak

Date :   22 Jul 09 (Deposition) - 18 Aug 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   3-Keto-L-Gulonate-6-Phosphate Decarboxylase, Ulad, Csgid, Niaid, Structural Genomics, National Institute Of Allergy And Infectious Diseases (Niaid), Center For Structural Genomics Of Infectious Diseases, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Nocek, N. Maltseva, J. Osipiuk, J. Stam, W. Anderson, A. Joachimiak
Crystal Structure Of 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961
To Be Published
PubMed: search

Molecule 1 - HEXULOSE-6-PHOSPHATE SYNTHASE SGBH
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PMCSG19C
	Gene	:	VC_A0242
	Organism Scientific	:	VIBRIO CHOLERAE
	Organism Taxid	:	666
	Strain	:	N16961

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C		E
Biological Unit 3 (2x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 57)

No.	Name	Count	Type	Full Name
1	GOL	10	Ligand/Ion	GLYCEROL
2	MSE	30	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	17	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 22)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 23)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 24)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:67 , GLY A:68 , GLY A:69 , ALA A:70 , THR A:94 , ALA A:97 , HOH A:223 , HOH A:544 , HOH A:547 , ARG B:139	BINDING SITE FOR RESIDUE SO4 A 1001
02	AC2	SOFTWARE	ALA A:88 , ALA A:90 , HIS A:91 , ILE A:92 , ILE A:95 , TRP A:125 , HOH A:625	BINDING SITE FOR RESIDUE GOL A 2001
03	AC3	SOFTWARE	ALA A:26 , ASN A:53 , HIS A:54 , PRO A:55 , ASN A:56 , HIS A:57	BINDING SITE FOR RESIDUE SO4 A 216
04	AC4	SOFTWARE	GLY A:170 , GLY A:171 , HOH A:633	BINDING SITE FOR RESIDUE SO4 A 217
05	AC5	SOFTWARE	HIS B:54 , PRO B:55 , ASN B:56 , HIS B:57	BINDING SITE FOR RESIDUE SO4 B 1002
06	AC6	SOFTWARE	GLN B:12 , THR B:13 , ARG B:192 , HOH B:373 , HOH B:634	BINDING SITE FOR RESIDUE GOL B 2001
07	AC7	SOFTWARE	ALA B:88 , ALA B:90 , HIS B:91 , ILE B:92 , ASP B:121 , TRP B:125	BINDING SITE FOR RESIDUE GOL B 2002
08	AC8	SOFTWARE	ILE B:113 , TRP B:117 , TYR B:135 , HIS B:136 , ARG B:137 , HOH B:472	BINDING SITE FOR RESIDUE GOL B 2003
09	AC9	SOFTWARE	ARG A:139 , ASP B:67 , GLY B:68 , GLY B:69 , ALA B:70 , THR B:94 , ALA B:97 , HOH B:649	BINDING SITE FOR RESIDUE SO4 B 216
10	BC1	SOFTWARE	GLY B:170 , GLY B:171 , ALA B:190 , GLY B:191 , HOH B:223	BINDING SITE FOR RESIDUE SO4 B 217
11	BC2	SOFTWARE	ALA C:88 , ALA C:90 , HIS C:91 , ILE C:92 , TRP C:125 , HOH C:287	BINDING SITE FOR RESIDUE GOL C 2001
12	BC3	SOFTWARE	ILE C:113 , TYR C:135 , HIS C:136 , SER C:138 , HOH C:246 , HOH C:482	BINDING SITE FOR RESIDUE GOL C 2002
13	BC4	SOFTWARE	HIS C:54 , PRO C:55 , ASN C:56 , HIS C:57 , HOH C:688 , HOH C:689	BINDING SITE FOR RESIDUE SO4 C 216
14	BC5	SOFTWARE	ASP C:67 , GLY C:68 , GLY C:69 , ALA C:70 , ALA C:93 , THR C:94 , ALA C:97 , HOH C:271 , HOH C:390 , HOH C:523 , ARG E:139	BINDING SITE FOR RESIDUE SO4 C 217
15	BC6	SOFTWARE	GLY C:170 , GLY C:171 , GLY C:191 , HOH C:228 , HOH C:303 , HOH C:467 , HOH C:681	BINDING SITE FOR RESIDUE SO4 C 218
16	BC7	SOFTWARE	ARG C:192 , HOH C:288	BINDING SITE FOR RESIDUE SO4 C 219
17	BC8	SOFTWARE	ARG D:51 , ASN D:56 , HIS D:57 , ASP D:82	BINDING SITE FOR RESIDUE GOL D 2001
18	BC9	SOFTWARE	ALA D:88 , ALA D:89 , ALA D:90 , ILE D:95 , TRP D:125 , HOH D:587 , HOH D:760	BINDING SITE FOR RESIDUE GOL D 2003
19	CC1	SOFTWARE	GLY D:191 , ARG D:192 , HOH D:301	BINDING SITE FOR RESIDUE SO4 D 216
20	CC2	SOFTWARE	ARG B:192 , HIS D:54 , PRO D:55 , ASN D:56 , HIS D:57 , HOH D:524 , HOH D:616	BINDING SITE FOR RESIDUE SO4 D 217
21	CC3	SOFTWARE	ASP D:67 , GLY D:68 , GLY D:69 , ALA D:70 , THR D:94 , ALA D:97 , ARG D:139 , HOH D:260 , HOH D:615	BINDING SITE FOR RESIDUE SO4 D 218
22	CC4	SOFTWARE	GLY D:170 , GLY D:171 , HOH D:286 , HOH D:540 , HOH D:541	BINDING SITE FOR RESIDUE SO4 D 219
23	CC5	SOFTWARE	ALA E:88 , ALA E:90 , HIS E:91 , ILE E:92 , ILE E:95 , ASP E:121 , TRP E:125 , HOH E:260	BINDING SITE FOR RESIDUE GOL E 2001
24	CC6	SOFTWARE	ILE E:113 , TRP E:117 , TYR E:135 , HIS E:136 , HOH E:229 , HOH E:282	BINDING SITE FOR RESIDUE GOL E 2002
25	CC7	SOFTWARE	ARG C:139 , ASP E:67 , GLY E:68 , GLY E:69 , ALA E:70 , THR E:94 , ALA E:97 , HOH E:233 , HOH E:488 , HOH E:617	BINDING SITE FOR RESIDUE SO4 E 216
26	CC8	SOFTWARE	ARG A:192 , ASN E:53 , HIS E:54 , PRO E:55 , ASN E:56 , HIS E:57	BINDING SITE FOR RESIDUE SO4 E 217
27	CC9	SOFTWARE	GLY E:170 , GLY E:171 , ALA E:190 , GLY E:191 , HOH E:423 , HOH E:442 , HOH E:458 , HOH E:608 , HOH E:721	BINDING SITE FOR RESIDUE SO4 E 218

(no "SS Bond" information available for 3IEB)

Asymmetric Unit

No.	Residues
1	Trp B:214	-	Pro B:215

(no "SAP(SNP)/Variant" information available for 3IEB)

(no "PROSITE Motif" information available for 3IEB)

(no "Exon" information available for 3IEB)

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:213
 aligned with Q9KMS8_VIBCH | Q9KMS8 from UniProtKB/TrEMBL  Length:215

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         Q9KMS8_VIBCH     2 TKPMIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGMKAVSTLRHNHPNHILVCDMKTTDGGAILSRMAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTMQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKMRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFW 214
               SCOP domains d3ieba_ A: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains 3iebA00 A:2-214 Aldolase class I                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh...eeeee.hhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieb A   2 TKPmIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGmKAVSTLRHNHPNHILVCDmKTTDGGAILSRmAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTmQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKmRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFW 214
                               |    11        21        31        41  |     51        61 |      71   |    81        91       101       111       121       131       141       151    |  161       171       181       191       201       211   
                               |                                     44-MSE             63-MSE      75-MSE                                     119-MSE                              156-MSE                                                      
                               5-MSE

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with Q9KMS8_VIBCH | Q9KMS8 from UniProtKB/TrEMBL  Length:215

    Alignment length:214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
         Q9KMS8_VIBCH     2 TKPMIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGMKAVSTLRHNHPNHILVCDMKTTDGGAILSRMAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTMQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKMRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
               SCOP domains d3iebb_ B: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 3iebB00 B:2-215 Aldolase class I                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh...eeeee.hhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieb B   2 TKPmIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGmKAVSTLRHNHPNHILVCDmKTTDGGAILSRmAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTmQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKmRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
                               |    11        21        31        41  |     51        61 |      71   |    81        91       101       111       121       131       141       151    |  161       171       181       191       201       211    
                               5-MSE                                 44-MSE             63-MSE      75-MSE                                     119-MSE                              156-MSE

Chain C from PDB  Type:PROTEIN  Length:214
 aligned with Q9KMS8_VIBCH | Q9KMS8 from UniProtKB/TrEMBL  Length:215

    Alignment length:214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
         Q9KMS8_VIBCH     2 TKPMIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGMKAVSTLRHNHPNHILVCDMKTTDGGAILSRMAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTMQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKMRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
               SCOP domains d3iebc_ C: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 3iebC00 C:2-215 Aldolase class I                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhh...eeeee.hhhhhhh....hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieb C   2 TKPmIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGmKAVSTLRHNHPNHILVCDmKTTDGGAILSRmAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTmQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKmRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
                               |    11        21        31        41  |     51        61 |      71   |    81        91       101       111       121       131       141       151    |  161       171       181       191       201       211    
                               5-MSE                                 44-MSE             63-MSE      75-MSE                                     119-MSE                              156-MSE

Chain D from PDB  Type:PROTEIN  Length:213
 aligned with Q9KMS8_VIBCH | Q9KMS8 from UniProtKB/TrEMBL  Length:215

    Alignment length:213
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   
         Q9KMS8_VIBCH     3 KPMIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGMKAVSTLRHNHPNHILVCDMKTTDGGAILSRMAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTMQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKMRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
               SCOP domains d3iebd_ D: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains 3iebD00 D:3-215 Aldolase class I                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh...eeeee.hhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieb D   3 KPmIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGmKAVSTLRHNHPNHILVCDmKTTDGGAILSRmAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTmQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKmRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
                              |     12        22        32        42 |      52        62|       72  |     82        92       102       112      |122       132       142       152   |   162       172       182       192       202       212   
                              5-MSE                                 44-MSE             63-MSE      75-MSE                                     119-MSE                              156-MSE

Chain E from PDB  Type:PROTEIN  Length:214
 aligned with Q9KMS8_VIBCH | Q9KMS8 from UniProtKB/TrEMBL  Length:215

    Alignment length:214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
         Q9KMS8_VIBCH     2 TKPMIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGMKAVSTLRHNHPNHILVCDMKTTDGGAILSRMAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTMQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKMRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
               SCOP domains d3iebe_ E: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 3iebE00 E:2-215 Aldolase class I                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhh...eeeee.hhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieb E   2 TKPmIQIALDQTNLTDAVAVASNVASYVDVIEVGTILAFAEGmKAVSTLRHNHPNHILVCDmKTTDGGAILSRmAFEAGADWITVSAAAHIATIAACKKVADELNGEIQIEIYGNWTmQDAKAWVDLGITQAIYHRSRDAELAGIGWTTDDLDKmRQLSALGIELSITGGIVPEDIYLFEGIKTKTFIAGRALAGAEGQQTAAALREQIDRFWP 215
                               |    11        21        31        41  |     51        61 |      71   |    81        91       101       111       121       131       141       151    |  161       171       181       191       201       211    
                               5-MSE                                 44-MSE             63-MSE      75-MSE                                     119-MSE                              156-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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: automated matches (38)

Protein domain: automated matches (38)

Vibrio cholerae [TaxId: 666] (2)

1a	d3ieba_	A:
1b	d3iebb_	B:
1c	d3iebc_	C:
1d	d3iebd_	D:
1e	d3iebe_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Vibrio cholerae. Organism_taxid: 666. Strain: n16961. (2)

1a	3iebB00	B:2-215
1b	3iebC00	C:2-215
1c	3iebE00	E:2-215
1d	3iebA00	A:2-214
1e	3iebD00	D:3-215

(no "Pfam Domain" information available for 3IEB)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (Q9KMS8_VIBCH | Q9KMS8)

molecular function
	GO:0016832	aldehyde-lyase activity	Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004590	orotidine-5'-phosphate decarboxylase activity	Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
biological process
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	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: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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]
		CC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Trp B:214 - Pro B:215	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3ieb
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q9KMS8_VIBCH \| Q9KMS8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q9KMS8_VIBCH \| Q9KMS8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q9KMS8_VIBCH \| Q9KMS8	:	3jr2

(no "Related Entries Specified in the PDB File" available for 3IEB)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 57)

Sites (27, 27)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 5)

CATH Domains (1, 5)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File