1VGW - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE

Authors :   Structural Genomix

Date :   03 Nov 03 (Deposition) - 25 Nov 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Structural Genomics, Transferase (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 - 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	2.7.7.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YGBP
	Organism Scientific	:	NEISSERIA GONORRHOEAE
	Organism Taxid	:	485

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1VGW)

(no "Site" information available for 1VGW)

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

Asymmetric Unit

No.	Residues
1	Thr A:166	-	Pro A:167
2	Thr B:166	-	Pro B:167
3	Thr C:166	-	Pro C:167
4	Thr D:166	-	Pro D:167
5	Thr E:166	-	Pro E:167
6	Thr F:166	-	Pro F:167

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPD	PS01295	4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.	ISPD_NEIG1	105-112	6	A:105-112 B:105-112 C:105-112 D:105-112 E:105-112 F:105-112

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPD	PS01295	4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.	ISPD_NEIG1	105-112	2	A:105-112 B:105-112 - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPD	PS01295	4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.	ISPD_NEIG1	105-112	2	- - C:105-112 D:105-112 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPD	PS01295	4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.	ISPD_NEIG1	105-112	2	- - - - E:105-112 F:105-112

(no "Exon" information available for 1VGW)

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 ISPD_NEIG1 | Q5F829 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      
           ISPD_NEIG1     2 KRKNIALIPAAGIGVRFGADKPKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAAENLGGITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLN 227
               SCOP domains d1vgwa_ A:           4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                      SCOP domains
               CATH domains 1vgwA00 A:2          -227 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..----------.....ee..eehhhhhhhhhhh.....eeeee......hhhhhhhhh...eee.....hhhhhhhhhhhhhhhhh......eeee........hhhhhhhhhhhhh.....eeeeee....eeee....eeeee....eeeeeeeeeeehhhhhhhhhh----...hhhhhhhh.....eeee.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgw A   2 KRKNIALIPAA----------PKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAA----GITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLD 227
                                    11|        - |      31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181    |  191       201       211       221      
                                     12         23                                                                                                                                                           181  186

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with ISPD_NEIG1 | Q5F829 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
           ISPD_NEIG1     1 MKRKNIALIPAAGIGVRFGADKPKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAAENLGGITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLN 227
               SCOP domains d1vgwb_ B: 4           -diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                      SCOP domains
               CATH domains 1vgwB00 B:1-           227 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..-----------.........hhhhhhhhhhhh.....eeeee.....hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhh.....eeeeee....eeee....eeeee....eeeeeeeeeeehhhhhhhh..--.....hhhhhhhh.....eeee.........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgw B   1 LKRKNIALIPAA-----------KQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAA--LGGITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLD 227
                                    10 |       -   |    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|  |   190       200       210       220       
                                      12          24                                                                                                                                                          181  |                                           
                                                                                                                                                                                                                 184

Chain C from PDB  Type:PROTEIN  Length:214
 aligned with ISPD_NEIG1 | Q5F829 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:228
                             1                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        
           ISPD_NEIG1     - -MKRKNIALIPAAGIGVRFGADKPKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAAENLGGITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLN 227
               SCOP domains d1vgwc_ C: 4-d         iphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                         SCOP domains
               CATH domains 1vgwC00 C:0-22         7 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee...---------..........hhhhhhhhhhhh.....eeeee......hhhhhhhhh...eee.....hhhhhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhh.....eeeeee....eeee....eeeee....eeeeeeeeeeehhhhhhhh..-----..hhhhhhhh.....eeee.........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vgw C   0 SLKRKNIALIPAAG---------PKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAA-----ITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLD 227
                                     9   |     -   |    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179 |     189       199       209       219        
                                        13        23                                                                                                                                                           181   187

Chain D from PDB  Type:PROTEIN  Length:211
 aligned with ISPD_NEIG1 | Q5F829 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
           ISPD_NEIG1     3 RKNIALIPAAGIGVRFGADKPKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAAENLGGITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLN 227
               SCOP domains d1vgwd_ D:           4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                     SCOP domains
               CATH domains 1vgwD00 D:          3-227 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.----------hhhh.ee..eehhhhhhhhhhh.....eeeeee.....hhhhhhhhh...eee.....hhhhhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhh.....eeeeee....eeee....eeeee....eeeeeeeeeeehhhhhhhh..----...hhhhhhhh.....eeee.........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgw D   3 RKNIALIPAA----------PKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAA----GITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLD 227
                                    12         -|       32        42        52        62        72        82        92       102       112       122       132       142       152       162       172        |-   |   192       202       212       222     
                                    12         23                                                                                                                                                           181  186

Chain E from PDB  Type:PROTEIN  Length:213
 aligned with ISPD_NEIG1 | Q5F829 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:228
                             1                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        
           ISPD_NEIG1     - -MKRKNIALIPAAGIGVRFGADKPKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAAENLGGITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLN 227
               SCOP domains d1vgwe_ E: 4-d         iphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                         SCOP domains
               CATH domains 1vgwE00 E:0-22         7 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee...---------.....ee..eehhhhhhhhhhh.....eeeee......hhhhhhhhh...eee.....hhhhhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhh.....eeeeee....eeee....eeeee....eeeeeeeeeeehhhhhhhhh------..hhhhhhhh.....eeee.........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vgw E   0 SLKRKNIALIPAAG---------PKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALA------ITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLD 227
                                     9   |     -   |    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179|      189       199       209       219        
                                        13        23                                                                                                                                                          180    187

Chain F from PDB  Type:PROTEIN  Length:209
 aligned with ISPD_NEIG1 | Q5F829 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      
           ISPD_NEIG1     2 KRKNIALIPAAGIGVRFGADKPKQYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALAAENLGGITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLN 227
               SCOP domains d1vgwf_ F:             4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                    SCOP domains
               CATH domains 1vgwF00 F:2            -227 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                           CATH domains
           Pfam domains (1) ---IspD-1vg            wF01 F:5-227                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ---IspD-1vg            wF02 F:5-227                                                                                                                                                                                                Pfam domains (2)
           Pfam domains (3) ---IspD-1vg            wF03 F:5-227                                                                                                                                                                                                Pfam domains (3)
           Pfam domains (4) ---IspD-1vg            wF04 F:5-227                                                                                                                                                                                                Pfam domains (4)
           Pfam domains (5) ---IspD-1vg            wF05 F:5-227                                                                                                                                                                                                Pfam domains (5)
           Pfam domains (6) ---IspD-1vg            wF06 F:5-227                                                                                                                                                                                                Pfam domains (6)
         Sec.struct. author ...eeeeee..------------...ee..eehhhhhhhhhhh.....eeeee......hhhhhhhhh...eee.....hhhhhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhh.....eeeeee....eeee....eeeee....eeeeeeeeeeehhhhhhhh.-----...hhhhhhhh.....eeee.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgw F   2 KRKNIALIPAA------------QYVEIGSKTVLEHVLGIFERHEAVDLTVVVVSPEDTFADKVQTAFPQVRVWKNGGQTRAETVRNGVAKLLETGLAAETDNILVHDAARCCLPSEALARLIEQAGNAAEGGILAVPVADTLKRAESGQISATVDRSGLWQAQTPQLFQAGLLHRALA-----GITDEASAVEKLGVRPLLIQGDARNLKLTQPQDAYIVRLLLD 227
                                    11|        -   |    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        |-    |  191       201       211       221      
                                     12           25                                                                                                                                                        180   186

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: Nucleotide-diphospho-sugar transferases (408)

Superfamily: Nucleotide-diphospho-sugar transferases (408)

Family: Cytidylytransferase (43)

Protein domain: 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP) (16)

Neisseria gonorrhoeae [TaxId: 485] (2)

1a	d1vgwa_	A:
1b	d1vgwb_	B:
1c	d1vgwc_	C:
1d	d1vgwd_	D:
1e	d1vgwe_	E:
1f	d1vgwf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A (231)

Homologous Superfamily: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A (231)

Neisseria gonorrhoeae. Organism_taxid: 485. (2)

1a	1vgwB00	B:1-227
1b	1vgwC00	C:0-227
1c	1vgwE00	E:0-227
1d	1vgwA00	A:2-227
1e	1vgwD00	D:3-227
1f	1vgwF00	F:2-227

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-A (172)

Family: IspD (16)

Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (2)

1a	IspD-1vgwF01	F:5-227
1b	IspD-1vgwF02	F:5-227
1c	IspD-1vgwF03	F:5-227
1d	IspD-1vgwF04	F:5-227
1e	IspD-1vgwF05	F:5-227
1f	IspD-1vgwF06	F:5-227

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (ISPD_NEIG1 | Q5F829)

molecular function
	GO:0050518	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0016114	terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1vgw)

	Sites
(no "Sites" information available for 1vgw)

	Cis Peptide Bonds
		Thr A:166 - Pro A:167	[ RasMol ]
		Thr B:166 - Pro B:167	[ RasMol ]
		Thr C:166 - Pro C:167	[ RasMol ]
		Thr D:166 - Pro D:167	[ RasMol ]
		Thr E:166 - Pro E:167	[ RasMol ]
		Thr F:166 - Pro F:167	[ 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 \| Biol. Unit 1 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
	1vgw
		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
	ISPD_NEIG1 \| Q5F829
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.7.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	ISPD_NEIG1 \| Q5F829
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	ISPD_NEIG1 \| Q5F829	:	1vgz

(no "Related Entries Specified in the PDB File" available for 1VGW)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 6)

CATH Domains (1, 6)

Pfam Domains (1, 6)

Gene Ontology (7, 7)

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Related Entries Specified in the PDB File