3MLA - JenaLib

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Title :   BANADD IN COMPLEX WITH INHIBITOR 1_02

Authors :   N. Huang, Y. Eyobo, H. Zhang

Date :   16 Apr 10 (Deposition) - 28 Jul 10 (Release) - 11 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Nmnat-Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Huang, R. Kolhatkar, Y. Eyobo, L. Sorci, I. Rodionova, A. L. Osterman, A. D. Mackerell, H. Zhang
Complexes Of Bacterial Nicotinate Mononucleotide Adenylyltransferase With Inhibitors: Implication For Structure-Based Drug Design And Improvement.
J. Med. Chem. V. 53 5229 2010
PubMed-ID: 20578699 | Reference-DOI: 10.1021/JM100377F

Molecule 1 - NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.7.7.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BAMEG_4595, NADD
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	1392
	Synonym	:	DEAMIDO-NAD(+) PYROPHOSPHORYLASE, DEAMIDO-NAD(+) DIPHOSPHORYLASE, NICOTINATE MONONUCLEOTIDE ADENYLYLTRANSFERASE, NAMN ADENYLYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
2	FMT	5	Ligand/Ion	FORMIC ACID
3	JJZ	1	Ligand/Ion	4-[2-(ANTHRACEN-9-YLMETHYLIDENE)HYDRAZINO]-N-(3-CHLOROPHENYL)-4-OXOBUTANAMIDE

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
2	FMT	5	Ligand/Ion	FORMIC ACID
3	JJZ	1	Ligand/Ion	4-[2-(ANTHRACEN-9-YLMETHYLIDENE)HYDRAZINO]-N-(3-CHLOROPHENYL)-4-OXOBUTANAMIDE

Biological Unit 2 (3, 16)

No.	Name	Count	Type	Full Name
1	DMS	4	Ligand/Ion	DIMETHYL SULFOXIDE
2	FMT	10	Ligand/Ion	FORMIC ACID
3	JJZ	2	Ligand/Ion	4-[2-(ANTHRACEN-9-YLMETHYLIDENE)HYDRAZINO]-N-(3-CHLOROPHENYL)-4-OXOBUTANAMIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:7 , GLY A:8 , ILE A:21 , PHE A:103 , ILE A:104 , ILE A:105 , GLY A:106 , MET A:109 , TYR A:112 , LYS A:115 , TRP A:116 , VAL A:131 , FMT A:194 , HOH A:196 , HOH A:235 , HOH A:316 , HOH A:319 , HOH A:345 , HOH A:355 , ILE B:7 , GLY B:8 , HIS B:18 , ILE B:21 , THR B:85 , PHE B:103 , ILE B:104 , ILE B:105 , GLY B:106 , MET B:109 , TYR B:112 , LYS B:115 , TRP B:116 , FMT B:192 , HOH B:285 , HOH B:319	BINDING SITE FOR RESIDUE JJZ A 190
2	AC2	SOFTWARE	ILE B:72 , HOH B:256	BINDING SITE FOR RESIDUE FMT B 190
3	AC3	SOFTWARE	TYR A:84	BINDING SITE FOR RESIDUE FMT A 191
4	AC4	SOFTWARE	TYR A:84 , HOH A:202 , HOH A:227 , ASN B:118	BINDING SITE FOR RESIDUE FMT A 192
5	AC5	SOFTWARE	TRP A:35 , SER A:71 , ILE A:72 , TYR A:96 , HOH A:216 , HOH A:217	BINDING SITE FOR RESIDUE DMS A 193
6	AC6	SOFTWARE	ARG A:183 , HOH A:320 , PRO B:82 , TYR B:84 , HOH B:296 , HOH B:327	BINDING SITE FOR RESIDUE DMS B 191
7	AC7	SOFTWARE	THR A:85 , TRP A:116 , JJZ A:190 , HOH A:215 , LYS B:115 , HOH B:216	BINDING SITE FOR RESIDUE FMT A 194
8	AC8	SOFTWARE	LYS A:115 , JJZ A:190 , HOH A:258 , THR B:85 , TRP B:116 , HOH B:202	BINDING SITE FOR RESIDUE FMT B 192

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

Asymmetric Unit

No.	Residues
1	Asp A:12	-	Pro A:13
2	Asp B:12	-	Pro B:13

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

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

(no "Exon" information available for 3MLA)

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:188
 aligned with NADD_BACAC | C3L5T6 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
           NADD_BACAC     1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYE 188
               SCOP domains d3mlaa_ A: automated matches                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhh..eeeeeeee.hhhhhhhhh.hhhhhhh..eeeeee............eeee......hhhhhhhhhhh........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mla A   1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYE 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with NADD_BACAC | C3L5T6 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
           NADD_BACAC     1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYES 189
               SCOP domains d3mlab_ B: automated matches                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee.....-----...hhhhhhhhhhhhhh....eee.hhhhhh....hhhhhhhhhhhhh..eeeeeeee..hhhhhhhh.hhhhhhh..eeeeee............eeee......hhhhhhhhhhh........hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mla B   1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPP-----NITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYES 189
                                    10        20        30        40  |     50        60        70        80        90       100       110       120       130       140       150       160       170       180         
                                                                     43    49

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: Adenine nucleotide alpha hydrolase-like (440)

Superfamily: Nucleotidylyl transferase (325)

Family: Adenylyltransferase (56)

Protein domain: automated matches (7)

Anthrax bacillus (Bacillus anthracis) [TaxId: 1392] (5)

1a	d3mlaa_	A:
1b	d3mlab_	B:

(no "CATH Domain" information available for 3MLA)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (NADD_BACAC | C3L5T6)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0004515	nicotinate-nucleotide adenylyltransferase activity	Catalysis of the reaction: ATP + nicotinate ribonucleotide = diphosphate + deamido-NAD+.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0009435	NAD biosynthetic process	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
	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:0019363	pyridine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

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	Cis Peptide Bonds
		Asp A:12 - Pro A:13	[ RasMol ]
		Asp B:12 - Pro B:13	[ RasMol ]

Biological Units
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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