4P8T - JenaLib

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Title :   CRYSTAL STRUCTURE OF M. TUBERCULOSIS DPRE1 IN COMPLEX WITH THE NON-COVALENT INHIBITOR QN129

Authors :   J. Neres, F. Pojer, S. T. Cole

Date :   01 Apr 14 (Deposition) - 10 Dec 14 (Release) - 01 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Dpre1, Inhibitor, Complex, Non-Covalent, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Neres, R. C. Hartkoorn, L. R. Chiarelli, R. Gadupudi, M. R. Pasca, G. Mori, A. Venturelli, S. Savina, V. Makarov, G. S. Kolly, E. Molteni, C. Binda, N. Dhar, S. Ferrari, P. Brodin, V. Delorme, V. Landry, A. L. De Jesus Lopes Ribeiro, D. Farina, P. Saxena, F. Pojer, A. Carta, R. Luciani, A. Porta, G. Zanoni, E. De Rossi, M. P. Costi, G. Riccardi, S. T. Cole
2-Carboxyquinoxalines Kill Mycobacterium Tuberculosis Through Noncovalent Inhibition Of Dpre1.
Acs Chem. Biol. V. 10 705 2015
PubMed-ID: 25427196 | Reference-DOI: 10.1021/CB5007163

Molecule 1 - PROBABLE DECAPRENYLPHOSPHORYL-BETA-D-RIBOSE OXIDASE
	Chains	:	A, B
	EC Number	:	1.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DPRE1, RV3790, MT3898
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	DPRE1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	2J3	1	Ligand/Ion	(2R)-2-{[(2R)-2-{[(2R)-2-HYDROXYPROPYL]OXY}PROPYL]OXY}PROPAN-1-OL
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	IMD	1	Ligand/Ion	IMIDAZOLE
4	R26	2	Ligand/Ion	3-[(4-CYANOBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	2J3	1	Ligand/Ion	(2R)-2-{[(2R)-2-{[(2R)-2-HYDROXYPROPYL]OXY}PROPYL]OXY}PROPAN-1-OL
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	IMD	1	Ligand/Ion	IMIDAZOLE
4	R26	1	Ligand/Ion	3-[(4-CYANOBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	2J3	-1	Ligand/Ion	(2R)-2-{[(2R)-2-{[(2R)-2-HYDROXYPROPYL]OXY}PROPYL]OXY}PROPAN-1-OL
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	IMD	-1	Ligand/Ion	IMIDAZOLE
4	R26	1	Ligand/Ion	3-[(4-CYANOBENZYL)AMINO]-6-(TRIFLUOROMETHYL)QUINOXALINE-2-CARBOXYLIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:16 , ILE A:52 , ALA A:53 , GLY A:55 , LEU A:56 , GLY A:57 , ARG A:58 , SER A:59 , TYR A:60 , ASN A:63 , ALA A:64 , MET A:74 , ALA A:94 , PRO A:116 , GLY A:117 , THR A:118 , VAL A:121 , THR A:122 , GLY A:124 , GLY A:125 , ALA A:128 , CYS A:129 , ILE A:131 , HIS A:132 , ASN A:178 , GLY A:179 , GLY A:182 , ILE A:184 , TYR A:415 , ALA A:417 , R26 A:502 , HOH A:630 , HOH A:644	binding site for residue FAD A 501
2	AC2	SOFTWARE	TYR A:60 , HIS A:132 , GLY A:133 , LYS A:134 , SER A:228 , TRP A:230 , ARG A:325 , GLN A:334 , GLN A:336 , LEU A:363 , ASN A:364 , VAL A:365 , LYS A:367 , ASN A:385 , CYS A:387 , LYS A:418 , FAD A:501 , 2J3 A:504	binding site for residue R26 A 502
3	AC3	SOFTWARE	SER A:82 , ASP A:84 , ASP B:84	binding site for residue IMD A 503
4	AC4	SOFTWARE	LYS A:134 , SER A:228 , ALA A:229 , TRP A:230 , ALA A:244 , TYR A:314 , PRO A:316 , R26 A:502	binding site for residue 2J3 A 504
5	AC5	SOFTWARE	TRP B:16 , ILE B:52 , ALA B:53 , ARG B:54 , GLY B:55 , LEU B:56 , GLY B:57 , ARG B:58 , SER B:59 , TYR B:60 , ASN B:63 , ALA B:64 , MET B:74 , ALA B:94 , PRO B:116 , GLY B:117 , THR B:118 , VAL B:121 , THR B:122 , GLY B:124 , GLY B:125 , ALA B:128 , CYS B:129 , ILE B:131 , HIS B:132 , ASN B:178 , GLY B:179 , GLY B:182 , ILE B:183 , ILE B:184 , TYR B:415 , ALA B:417 , R26 B:502 , HOH B:618	binding site for residue FAD B 501
6	AC6	SOFTWARE	TYR B:60 , HIS B:132 , GLY B:133 , LYS B:134 , TRP B:230 , LEU B:363 , ASN B:364 , VAL B:365 , LYS B:367 , ASN B:385 , CYS B:387 , LYS B:418 , FAD B:501	binding site for residue R26 B 502

(no "SS Bond" information available for 4P8T)

Asymmetric Unit

No.	Residues
1	Pro A:237	-	Pro A:238
2	Arg A:325	-	Ala A:326
3	Ala A:330	-	Gly A:331
4	Pro B:237	-	Pro B:238

(no "SAP(SNP)/Variant" information available for 4P8T)

(no "PROSITE Motif" information available for 4P8T)

(no "Exon" information available for 4P8T)

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:456
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee........eeeeeee..hhhhhhhhhhhhhhh.....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee....eeeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhh............hhhhhh..........hhhhhhhhhhhh.eeeeeeehhhhhh.hhhhh..........eeeeeeeee..hhhhhhhhhhhhhhh.......eeee..............eeeeeeeee...hhhhhhhhhhhhhhhh..ee........hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p8t A   6 ATTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPQLLTLPDVFPNGLANKYTFGPIGELWYRKSGTYRGKVQNLTQFYHPLDMFGEWNRAYGPAGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455

Chain B from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeeeee..hhhhhhhhhhhhhh......eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee.....eeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhh................hhhhhhhhhheeeeeehhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh.......eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee.hhhh...hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8t B   8 TTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPPIGELWYRKSGTYRGKVQNLTQFYHGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267  ||   297       307       332       342       352       362       372       382       392       402       412       422       432       442       452         
                                                                                                                                                                                                                                                                                                270|                     315|                                                                                                                                  
                                                                                                                                                                                                                                                                                                 291                      331

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 '\|'

(no "SCOP Domain" information available for 4P8T)

(no "CATH Domain" information available for 4P8T)

(no "Pfam Domain" information available for 4P8T)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		2J3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:330 - Gly A:331	[ RasMol ]
		Arg A:325 - Ala A:326	[ RasMol ]
		Pro A:237 - Pro A:238	[ RasMol ]
		Pro B:237 - Pro B:238	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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Gene Ontology (14, 23)

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