4D8A - JenaLib

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Title :   CRYSTAL STRUCTURE OF B. ANTHRACIS DHPS WITH COMPOUND 21

Authors :   D. Hammoudeh, R. E. Lee, S. W. White

Date :   10 Jan 12 (Deposition) - 04 Apr 12 (Release) - 09 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.18

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

Keywords :   Tim Barrel, Tim Narrel, Synthase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhao, D. Hammoudeh, M. K. Yun, J. Qi, S. W. White, R. E. Lee
Structure-Based Design Of Novel Pyrimido[4, 5-C]Pyridazine Derivatives As Dihydropteroate Synthase Inhibitors With Increased Affinity.
Chemmedchem V. 7 861 2012
PubMed-ID: 22416048 | Reference-DOI: 10.1002/CMDC.201200049

Molecule 1 - DIHYDROPTEROATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FOLP
	Organism Common	:	ANTHRAX
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	191218
	Strain	:	A2012

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	0HY	2	Ligand/Ion	METHYL (3R)-3-(7-AMINO-4,5-DIOXO-1,4,5,6-TETRAHYDROPYRIMIDO[4,5-C]PYRIDAZIN-3-YL)BUTANOATE
2	LYS	1	Mod. Amino Acid	LYSINE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	0HY	2	Ligand/Ion	METHYL (3R)-3-(7-AMINO-4,5-DIOXO-1,4,5,6-TETRAHYDROPYRIMIDO[4,5-C]PYRIDAZIN-3-YL)BUTANOATE
2	LYS	2	Mod. Amino Acid	LYSINE
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	0HY	2	Ligand/Ion	METHYL (3R)-3-(7-AMINO-4,5-DIOXO-1,4,5,6-TETRAHYDROPYRIMIDO[4,5-C]PYRIDAZIN-3-YL)BUTANOATE
2	LYS	-1	Mod. Amino Acid	LYSINE
3	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 12)

No.	Name	Count	Type	Full Name
1	0HY	2	Ligand/Ion	METHYL (3R)-3-(7-AMINO-4,5-DIOXO-1,4,5,6-TETRAHYDROPYRIMIDO[4,5-C]PYRIDAZIN-3-YL)BUTANOATE
2	LYS	-1	Mod. Amino Acid	LYSINE
3	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:17 , GLU A:18 , LYS A:19 , THR A:20 , CYS A:250 , ASP A:269 , ILE A:272 , GLY A:273 , HOH A:402 , HOH A:404	BINDING SITE FOR RESIDUE LYS A 301
02	AC2	SOFTWARE	LYS A:50 , ARG A:53	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	SER A:221 , ARG A:234	BINDING SITE FOR RESIDUE SO4 A 303
04	AC4	SOFTWARE	ARG A:219	BINDING SITE FOR RESIDUE SO4 A 304
05	AC5	SOFTWARE	ILE A:25 , ASP A:101 , ASN A:120 , ILE A:122 , ILE A:143 , MET A:145 , ASP A:184 , PHE A:189 , GLY A:216 , LYS A:220 , ARG A:254 , HIS A:256	BINDING SITE FOR RESIDUE 0HY A 305
06	AC6	SOFTWARE	SER B:221 , ARG B:234	BINDING SITE FOR RESIDUE SO4 B 301
07	AC7	SOFTWARE	ARG B:219	BINDING SITE FOR RESIDUE SO4 B 302
08	AC8	SOFTWARE	ARG B:201 , ASN B:202	BINDING SITE FOR RESIDUE SO4 B 303
09	AC9	SOFTWARE	LYS B:50 , ARG B:53	BINDING SITE FOR RESIDUE SO4 B 304
10	BC1	SOFTWARE	LEU B:229 , ARG B:263	BINDING SITE FOR RESIDUE SO4 B 305
11	BC2	SOFTWARE	ASP B:101 , ASN B:120 , ILE B:122 , ILE B:143 , MET B:145 , ASP B:184 , PHE B:189 , GLY B:216 , LYS B:220 , ARG B:254	BINDING SITE FOR RESIDUE 0HY B 306

(no "SS Bond" information available for 4D8A)

(no "Cis Peptide Bond" information available for 4D8A)

(no "SAP(SNP)/Variant" information available for 4D8A)

(no "PROSITE Motif" information available for 4D8A)

(no "Exon" information available for 4D8A)

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:264
 aligned with Q81VW8_BACAN | Q81VW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:273
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
         Q81VW8_BACAN     5 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESTRPGFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 277
               SCOP domains d4d8aa_ A: Dihydropteroate synthetase                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee......eeeee............hhhhhhhhhhhhhhhhhh...eeee.---------..hhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh..eeee.......hhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhhhhhhhhh...ee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d8a A   2 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIG---------KVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 301
                                    11        21        31        41        51        61 |       - |      81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271 ||
                                                                                        63        73                                                                                                                                                                                                     273|
                                                                                                                                                                                                                                                                                                          301

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with Q81VW8_BACAN | Q81VW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:273
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
         Q81VW8_BACAN     5 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESTRPGFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 277
               SCOP domains d4d8ab_ B: Dihydropteroate           synthetase                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee......eeeee..----------.hhhhhhhhhhhhhhhhhh..eeee.-----------.hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh..eeee.......hhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhh.hhh.eeee.......hhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d8a B   2 KWDYDLRCGEYTLNLNEKTLIMGILN----------SYNEVDAAVRHAKEMRDEGAHIIDIG-----------SVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 274
                                    11        21     |   -      | 41        51        61 |       -   |    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
                                                    27         38                       63          75

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: Dihydropteroate synthetase-like (59)

Family: Dihydropteroate synthetase (40)

Protein domain: Dihydropteroate synthetase (34)

Anthrax bacillus (Bacillus anthracis) [TaxId: 1392] (28)

1a	d4d8aa_	A:
1b	d4d8ab_	B:

(no "CATH Domain" information available for 4D8A)

(no "Pfam Domain" information available for 4D8A)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q81VW8_BACAN | Q81VW8)

molecular function
	GO:0004156	dihydropteroate synthase activity	Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0044237	cellular metabolic process	The chemical reactions and pathways by which individual cells transform chemical substances.
	GO:0046656	folic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
	GO:0009396	folic acid-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
	GO:0042558	pteridine-containing compound metabolic process	The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.
	GO:0046654	tetrahydrofolate biosynthetic process	The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4d8a)

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	4d8a
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	2.5.1.15
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (8, 8)

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