1VH8 - JenaLib

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 A 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE

Authors :   Structural Genomix

Date :   01 Dec 03 (Deposition) - 30 Dec 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,C  (1x)
Biol. Unit 2: D,E,F  (1x)
Biol. Unit 3: A (2x),B (2x),C (2x),D (2x),E (2x),F (2x)

Keywords :   Structural Genomics, Lyase (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 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	4.6.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ISPF, HI0671
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	MECPS, MECDP-SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 20)

No.	Name	Count	Type	Full Name
1	ACY	6	Ligand/Ion	ACETIC ACID
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	POP	2	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	ACY	3	Ligand/Ion	ACETIC ACID
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	ACY	3	Ligand/Ion	ACETIC ACID
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 3 (3, 20)

No.	Name	Count	Type	Full Name
1	ACY	6	Ligand/Ion	ACETIC ACID
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	POP	2	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:139 , PHE A:140 , ARG A:143 , ACY A:170 , GLY B:139 , PHE B:140 , ARG B:143 , ACY B:169 , GLY C:139 , PHE C:140 , ARG C:143 , ACY C:169	BINDING SITE FOR RESIDUE POP A 169
2	AC2	SOFTWARE	GLY D:139 , PHE D:140 , ARG D:143 , ACY D:170 , GLY E:139 , PHE E:140 , ARG E:143 , ACY E:169 , GLY F:139 , PHE F:140 , ARG F:143 , ACY F:169	BINDING SITE FOR RESIDUE POP D 169
3	AC3	SOFTWARE	PHE A:140 , THR A:141 , POP A:169 , ACY B:169 , ACY C:169	BINDING SITE FOR RESIDUE ACY A 170
4	AC4	SOFTWARE	POP A:169 , ACY A:170 , PHE B:140 , THR B:141 , ACY C:169	BINDING SITE FOR RESIDUE ACY B 169
5	AC5	SOFTWARE	POP A:169 , ACY A:170 , ACY B:169 , LEU C:138 , GLY C:139 , PHE C:140 , THR C:141	BINDING SITE FOR RESIDUE ACY C 169
6	AC6	SOFTWARE	PHE D:140 , THR D:141 , POP D:169 , ACY E:169 , ACY F:169	BINDING SITE FOR RESIDUE ACY D 170
7	AC7	SOFTWARE	POP D:169 , ACY D:170 , PHE E:140 , THR E:141	BINDING SITE FOR RESIDUE ACY E 169
8	AC8	SOFTWARE	POP D:169 , ACY D:170 , THR F:135 , LEU F:138 , PHE F:140 , THR F:141	BINDING SITE FOR RESIDUE ACY F 169

(no "SS Bond" information available for 1VH8)

(no "Cis Peptide Bond" information available for 1VH8)

(no "SAP(SNP)/Variant" information available for 1VH8)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_HAEIN	36-51	6	A:36-51 B:36-51 C:36-51 D:36-51 E:36-51 F:36-51

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_HAEIN	36-51	3	A:36-51 B:36-51 C:36-51 - - -

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_HAEIN	36-51	3	- - - D:36-51 E:36-51 F:36-51

Biological Unit 3 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_HAEIN	36-51	12	A:36-51 B:36-51 C:36-51 D:36-51 E:36-51 F:36-51

(no "Exon" information available for 1VH8)

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:153
 aligned with ISPF_HAEIN | P44815 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:159
                             1                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149         
           ISPF_HAEIN     - -MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
               SCOP domains d1vh8a_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase       IspF                                                                                      SCOP domains
               CATH domains 1vh8A00 A:0-158  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.eeeeeeee..eeeeeeee.......hhhhhhhhhhhhhhh...hhhhh..------...hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vh8 A   0 SLIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFP------KNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKmRPHIDAmRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
                                     9        19        29        39        49        59   |     -|       79        89        99      |109   |   119       129       139       149         
                                                                                          63     70                                 106-MSE  |                                             
                                                                                                                                           113-MSE

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with ISPF_HAEIN | P44815 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:159
                             1                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149         
           ISPF_HAEIN     - -MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
               SCOP domains d1vh8b_ B: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase        IspF                                                                                     SCOP domains
               CATH domains 1vh8B00 B:0-158  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeee..eeeeeee........hhhhhhhhhhhhhhh...hhhhh..-------..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vh8 B   0 SLIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFP-------NADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKmRPHIDAmRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
                                     9        19        29        39        49        59   |     - |      79        89        99      |109   |   119       129       139       149         
                                                                                          63      71                                106-MSE  |                                             
                                                                                                                                           113-MSE

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with ISPF_HAEIN | P44815 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:159
                             1                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149         
           ISPF_HAEIN     - -MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
               SCOP domains d1vh8c_ C: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase        IspF                                                                                     SCOP domains
               CATH domains 1vh8C00 C:0-158  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.eeeeeeee..eeeeeeee.......hhhhhhhhhhhhhhh...hhhhh..-------..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vh8 C   0 SLIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFP-------NADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKmRPHIDAmRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
                                     9        19        29        39        49        59   |     - |      79        89        99      |109   |   119       129       139       149         
                                                                                          63      71                                106-MSE  |                                             
                                                                                                                                           113-MSE

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with ISPF_HAEIN | P44815 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:159
                             1                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149         
           ISPF_HAEIN     - -MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
               SCOP domains d1vh8d_ D: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase        IspF                                                                                     SCOP domains
               CATH domains 1vh8D00 D:0-158  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.eeeeeeee..eeeeeeee.......hhhhhhhhhhhhhhh...hhhhh..-------..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vh8 D   0 SLIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFP-------NADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKmRPHIDAmRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
                                     9        19        29        39        49        59   |     - |      79        89        99      |109   |   119       129       139       149         
                                                                                          63      71                                106-MSE  |                                             
                                                                                                                                           113-MSE

Chain E from PDB  Type:PROTEIN  Length:152
 aligned with ISPF_HAEIN | P44815 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:159
                             1                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149         
           ISPF_HAEIN     - -MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
               SCOP domains d1vh8e_ E: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase        IspF                                                                                     SCOP domains
               CATH domains 1vh8E00 E:0-158  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeee..eeeeeee........hhhhhhhhhhhhhhh..........-------..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vh8 E   0 SLIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFP-------NADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKmRPHIDAmRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
                                     9        19        29        39        49        59   |     - |      79        89        99      |109   |   119       129       139       149         
                                                                                          63      71                                106-MSE  |                                             
                                                                                                                                           113-MSE

Chain F from PDB  Type:PROTEIN  Length:152
 aligned with ISPF_HAEIN | P44815 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:159
                             1                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149         
           ISPF_HAEIN     - -MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
               SCOP domains d1vh8f_ F: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase        IspF                                                                                     SCOP domains
               CATH domains 1vh8F00 F:0-158  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
           Pfam domains (1) --YgbB-1vh8F01 F:2-158                                                                                                                                          Pfam domains (1)
           Pfam domains (2) --YgbB-1vh8F02 F:2-158                                                                                                                                          Pfam domains (2)
           Pfam domains (3) --YgbB-1vh8F03 F:2-158                                                                                                                                          Pfam domains (3)
           Pfam domains (4) --YgbB-1vh8F04 F:2-158                                                                                                                                          Pfam domains (4)
           Pfam domains (5) --YgbB-1vh8F05 F:2-158                                                                                                                                          Pfam domains (5)
           Pfam domains (6) --YgbB-1vh8F06 F:2-158                                                                                                                                          Pfam domains (6)
         Sec.struct. author ..eeeeeeeeeee.eeeeeeee..eeeeeeee.......hhhhhhhhhhhhhhh...hhhhh..-------..hhhhhhhhhhhhhhh..eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vh8 F   0 SLIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFP-------NADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKmRPHIDAmRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIRQ 158
                                     9        19        29        39        49        59   |     - |      79        89        99      |109   |   119       129       139       149         
                                                                                          63      71                                106-MSE  |                                             
                                                                                                                                           113-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) (23004)

Fold: Bacillus chorismate mutase-like (324)

Superfamily: IpsF-like (56)

Family: IpsF-like (35)

Protein domain: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (27)

Haemophilus influenzae [TaxId: 727] (3)

1a	d1vh8a_	A:
1b	d1vh8b_	B:
1c	d1vh8c_	C:
1d	d1vh8d_	D:
1e	d1vh8e_	E:
1f	d1vh8f_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.50, no name defined] (46)

Haemophilus influenzae. Organism_taxid: 727. (3)

1a	1vh8A00	A:0-158
1b	1vh8B00	B:0-158
1c	1vh8C00	C:0-158
1d	1vh8D00	D:0-158
1e	1vh8E00	E:0-158
1f	1vh8F00	F:0-158

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: YgbB] (24)

Family: YgbB (24)

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (3)

1a	YgbB-1vh8F01	F:2-158
1b	YgbB-1vh8F02	F:2-158
1c	YgbB-1vh8F03	F:2-158
1d	YgbB-1vh8F04	F:2-158
1e	YgbB-1vh8F05	F:2-158
1f	YgbB-1vh8F06	F:2-158

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (ISPF_HAEIN | P44815)

molecular function
	GO:0008685	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity	Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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
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	Cis Peptide Bonds
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	1vh8
		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
	ISPF_HAEIN \| P44815
		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)
	4.6.1.12
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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

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		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
	ISPF_HAEIN \| P44815
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ISPF_HAEIN \| P44815	:	1jn1 1vha 5esv 5esz

(no "Related Entries Specified in the PDB File" available for 1VH8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (1, 6)

Pfam Domains (1, 6)

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