3KCQ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE FROM ANAPLASMA PHAGOCYTOPHILUM

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   21 Oct 09 (Deposition) - 15 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Structural Genomics, Niaid, Transferase, Seattle Structural Genomics Center For Infectious Disease, Ssgcid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. L. Staker, T. Edwards, M. Dieterich, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Phosphoribosylglycinamide Formyltransferase From Anaplasma Phagocytophilum
To Be Published
PubMed: search

Molecule 1 - PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.1.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PURN, APH_0230
	Organism Scientific	:	ANAPLASMA PHAGOCYTOPHILUM
	Organism Taxid	:	212042
	Strain	:	HZ

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:13 , ARG A:14 , GLY A:15 , SER A:16 , ASN A:17 , HOH A:215 , HOH A:216 , HOH A:233 , HOH A:238	BINDING SITE FOR RESIDUE GOL A 801
2	AC2	SOFTWARE	ARG B:14 , GLY B:15 , SER B:16 , ASN B:17 , HOH B:213 , HOH B:227 , HOH B:250	BINDING SITE FOR RESIDUE GOL B 801
3	AC3	SOFTWARE	GLY C:13 , ARG C:14 , GLY C:15 , ASN C:17 , GLY C:86 , HOH C:224 , HOH C:253 , HOH C:276	BINDING SITE FOR RESIDUE GOL C 801
4	AC4	SOFTWARE	ARG D:14 , GLY D:15 , SER D:16 , ASN D:17 , HOH D:215	BINDING SITE FOR RESIDUE GOL D 801

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

Asymmetric Unit

No.	Residues
1	Lys A:63	-	Pro A:64
2	Leu A:111	-	Pro A:112
3	Lys B:63	-	Pro B:64
4	Leu B:111	-	Pro B:112
5	Lys C:63	-	Pro C:64
6	Leu C:111	-	Pro C:112
7	Lys D:63	-	Pro D:64
8	Leu D:111	-	Pro D:112

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

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

(no "Exon" information available for 3KCQ)

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:207
 aligned with Q2GLA4_ANAPZ | Q2GLA4 from UniProtKB/TrEMBL  Length:211

    Alignment length:208
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        
         Q2GLA4_ANAPZ     3 KELRVGVLISGRGSNLEALAKAFSTEESSVVISCVISNNAEARGLLIAQSYGIPTFVVKRKPLDIEHISTVLREHDVDLVCLAGFMSILPEKFVTDWHHKIINIHPSLLPSFKGLNAQEQAYKAGVKIAGCTLHYVYQELDAGPIIMQAAVPVLREDTAESLASRILAAEHVCYPKGVKLIAQDKIKLCDDGTVQCTGEDELFLFQEN 210
               SCOP domains d3kcqa_ A: automated matc hes                                                                                                                                                                                    SCOP domains
               CATH domains 3kcqA00 A:3-210  [code=3. 40.50.170, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhh..-...eeeeeeee.....hhhhhhhhh...eee......hhhhhhhhhhhh...eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee......eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kcq A   3 KELRVGVLISGRGSNLEALAKAFST-ESSVVISCVISNNAEARGLLIAQSYGIPTFVVKRKPLDIEHISTVLREHDVDLVCLAGFMSILPEKFVTDWHHKIINIHPSLLPSFKGLNAQEQAYKAGVKIAGCTLHYVYQELDAGPIIMQAAVPVLREDTAESLASRILAAEHVCYPKGVKLIAQDKIKLCDDGTVQCTGEDELFLFQEN 210
                                    12        22    | | 32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        
                                                   27 |                                                                                                                                                                                     
                                                     29

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with Q2GLA4_ANAPZ | Q2GLA4 from UniProtKB/TrEMBL  Length:211

    Alignment length:207
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
         Q2GLA4_ANAPZ     3 KELRVGVLISGRGSNLEALAKAFSTEESSVVISCVISNNAEARGLLIAQSYGIPTFVVKRKPLDIEHISTVLREHDVDLVCLAGFMSILPEKFVTDWHHKIINIHPSLLPSFKGLNAQEQAYKAGVKIAGCTLHYVYQELDAGPIIMQAAVPVLREDTAESLASRILAAEHVCYPKGVKLIAQDKIKLCDDGTVQCTGEDELFLFQE 209
               SCOP domains d3kcqb_ B: automated matc   hes                                                                                                                                                                                 SCOP domains
               CATH domains 3kcqB00 B:3-209  [code=3.   40.50.170, no name defined]                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhh..---.eeeeeeee.....hhhhhhhhh...eee......hhhhhhhhhhhh...eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee......eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kcq B   3 KELRVGVLISGRGSNLEALAKAFST---SVVISCVISNNAEARGLLIAQSYGIPTFVVKRKPLDIEHISTVLREHDVDLVCLAGFMSILPEKFVTDWHHKIINIHPSLLPSFKGLNAQEQAYKAGVKIAGCTLHYVYQELDAGPIIMQAAVPVLREDTAESLASRILAAEHVCYPKGVKLIAQDKIKLCDDGTVQCTGEDELFLFQE 209
                                    12        22    |   32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
                                                   27  31

Chain C from PDB  Type:PROTEIN  Length:209
 aligned with Q2GLA4_ANAPZ | Q2GLA4 from UniProtKB/TrEMBL  Length:211

    Alignment length:209
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202         
         Q2GLA4_ANAPZ     3 KELRVGVLISGRGSNLEALAKAFSTEESSVVISCVISNNAEARGLLIAQSYGIPTFVVKRKPLDIEHISTVLREHDVDLVCLAGFMSILPEKFVTDWHHKIINIHPSLLPSFKGLNAQEQAYKAGVKIAGCTLHYVYQELDAGPIIMQAAVPVLREDTAESLASRILAAEHVCYPKGVKLIAQDKIKLCDDGTVQCTGEDELFLFQENF 211
               SCOP domains d3kcqc_ C: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains 3kcqC00 C:3-211  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhh.....eeeeeeee.....hhhhhhhhh...eee......hhhhhhhhhhhh...eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee......eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kcq C   3 KELRVGVLISGRGSNLEALAKAFSTEESSVVISCVISNNAEARGLLIAQSYGIPTFVVKRKPLDIEHISTVLREHDVDLVCLAGFMSILPEKFVTDWHHKIINIHPSLLPSFKGLNAQEQAYKAGVKIAGCTLHYVYQELDAGPIIMQAAVPVLREDTAESLASRILAAEHVCYPKGVKLIAQDKIKLCDDGTVQCTGEDELFLFQENF 211
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

Chain D from PDB  Type:PROTEIN  Length:204
 aligned with Q2GLA4_ANAPZ | Q2GLA4 from UniProtKB/TrEMBL  Length:211

    Alignment length:207
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
         Q2GLA4_ANAPZ     3 KELRVGVLISGRGSNLEALAKAFSTEESSVVISCVISNNAEARGLLIAQSYGIPTFVVKRKPLDIEHISTVLREHDVDLVCLAGFMSILPEKFVTDWHHKIINIHPSLLPSFKGLNAQEQAYKAGVKIAGCTLHYVYQELDAGPIIMQAAVPVLREDTAESLASRILAAEHVCYPKGVKLIAQDKIKLCDDGTVQCTGEDELFLFQE 209
               SCOP domains d3kcqd_ D: automated mat   ches                                                                                                                                                                                 SCOP domains
               CATH domains 3kcqD00 D:3-209  [code=3   .40.50.170, no name defined]                                                                                                                                                         CATH domains
           Pfam domains (1) --Formyl_trans_N-3kcqD01    D:5-180                                                                                                                                               ----------------------------- Pfam domains (1)
           Pfam domains (2) --Formyl_trans_N-3kcqD02    D:5-180                                                                                                                                               ----------------------------- Pfam domains (2)
           Pfam domains (3) --Formyl_trans_N-3kcqD03    D:5-180                                                                                                                                               ----------------------------- Pfam domains (3)
           Pfam domains (4) --Formyl_trans_N-3kcqD04    D:5-180                                                                                                                                               ----------------------------- Pfam domains (4)
         Sec.struct. author ..eeeeeee...hhhhhhhhhhh.---..eeeeeeee.....hhhhhhhhh...eee......hhhhhhhhhhhh...eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee......eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kcq D   3 KELRVGVLISGRGSNLEALAKAFS---SSVVISCVISNNAEARGLLIAQSYGIPTFVVKRKPLDIEHISTVLREHDVDLVCLAGFMSILPEKFVTDWHHKIINIHPSLLPSFKGLNAQEQAYKAGVKIAGCTLHYVYQELDAGPIIMQAAVPVLREDTAESLASRILAAEHVCYPKGVKLIAQDKIKLCDDGTVQCTGEDELFLFQE 209
                                    12        22   |   |32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
                                                  26  30

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: Formyltransferase (42)

Superfamily: Formyltransferase (42)

Family: automated matches (8)

Protein domain: automated matches (8)

Anaplasma phagocytophilum [TaxId: 212042] (1)

1a	d3kcqa_	A:
1b	d3kcqb_	B:
1c	d3kcqc_	C:
1d	d3kcqd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.170, no name defined] (28)

Anaplasma phagocytophilum hz. Organism_taxid: 212042. Strain: hz. (1)

1a	3kcqB00	B:3-209
1b	3kcqD00	D:3-209
1c	3kcqA00	A:3-210
1d	3kcqC00	C:3-211

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Formyl_trans_N] (25)

Family: Formyl_trans_N (25)

Anaplasma phagocytophilum (strain HZ) (1)

1a	Formyl_trans_N-3kcqD01	D:5-180
1b	Formyl_trans_N-3kcqD02	D:5-180
1c	Formyl_trans_N-3kcqD03	D:5-180
1d	Formyl_trans_N-3kcqD04	D:5-180

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q2GLA4_ANAPZ | Q2GLA4)

molecular function
	GO:0016742	hydroxymethyl-, formyl- and related transferase activity	Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
	GO:0004644	phosphoribosylglycinamide formyltransferase activity	Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
	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:0006189	'de novo' IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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