PDB Goodies - a web-based GUI to manipulate the Protein Data Bank file

PDB Goodies is a web-based graphical user interface (GUI) to manipulate the Protein Data Bank file containing the three-dimensional atomic coordinates of protein structures. The program also allows users to save the manipulated three-dimensional atomic coordinate file on their local client system. These fragments are used in various stages of structure elucidation and analysis. This software is incorporated with all the three-dimensional protein structures available in the Protein Data Bank, which presently holds approximately 18 000 structures. In addition, this program works on a three-dimensional atomic coordinate file (Protein Data Bank format) uploaded from the client machine. The program is written using CGI/PERL scripts and is platform independent. The program PDB Goodies can be accessed over the World Wide Web at http:// 144.16.71.11/pdbgoodies/.

Cloning, expression, purification and preliminary X-ray diffraction studies of a putative Mycobacterium smegmatis thiolase

Thiolases are important in fatty-acid degradation and biosynthetic pathways. Analysis of the genomic sequence of Mycobacterium smegmatis suggests the presence of several putative thiolase genes. One of these genes appears to code for an SCP-x protein. Human SCP-x consists of an N-terminal domain (referred to as SCP2 thiolase) and a C-terminal domain (referred as sterol carrier protein 2). Here, the cloning, expression, purification and crystallization of this putative SCP-x protein from M. smegmatis are reported. The crystals diffracted X-rays to 2.5 angstrom resolution and belonged to the triclinic space group P1. Calculation of rotation functions using X-ray diffraction data suggests that the protein is likely to possess a hexameric oligomerization with 32 symmetry which has not been observed in the other six known classes of this enzyme.

(4aR, 8aS, 9aR, 10aS)-8a, 9a-Difluoro-1,4,4a, 5,8,8a, 9,9a, 10,10a-decahydroanthracene-4a, 10a-diol hemihydrate

The title compound, C(14)H(18)F(2)O(2)center dot 0.5H(2)O, a hemihydrate of a C(s)-symmetric unsaturated difluorodiol, crystallizes in the centrosymmetric space group P2/m (Z = 4). The asymmetric unit contains two crystallographically independent difluorodiol half-molecules, occupying the mirror planes at (x, 0, z) and (x, 1/2, z), and half a molecule of water, lying on the twofold axis at (0, y, 0). Four difluorodiol molecules self-assemble around each solvent water molecule via O-H center dot center dot center dot O hydrogen bonds in a near tetrahedral symmetry to generate a cylindrical column-like architecture.

Location and conformation of pantothenate and its derivatives in Mycobacterium tuberculosis pantothenate kinase: insights into enzyme action

Previous studies of complexes of Mycobacterium tuberculosis PanK (MtPanK) with nucleotide diphosphates and non-hydrolysable analogues of nucleoside triphosphates in the presence or the absence of pantothenate established that the enzyme has dual specificity for ATP and GTP, revealed the unusual movement of ligands during enzyme action and provided information on the effect of pantothenate on the location and conformation of the nucleotides at the beginning and the end of enzyme action. The X-ray analyses of the binary complexes of MtPanK with pantothenate, pantothenol and N-nonylpantothenamide reported here demonstrate that in the absence of nucleotide these ligands occupy, with a somewhat open conformation, a location similar to that occupied by phosphopantothenate in the `end' complexes, which differs distinctly from the location of pantothenate in the closed conformation in the ternary `initiation' complexes. The conformation and the location of the nucleotide were also different in the initiation and end complexes. An invariant arginine appears to play a critical role in the movement of ligands that takes place during enzyme action. The work presented here completes the description of the locations and conformations of nucleoside diphosphates and triphosphates and pantothenate in different binary and ternary complexes, and suggests a structural rationale for the movement of ligands during enzyme action. The present investigation also suggests that N-alkylpantothenamides could be phosphorylated by the enzyme in the same manner as pantothenate.

3-(2-Bromoacetyl)-6-fluoro-2H-chromen-2-one

The non-H atoms of the title compound, C(11)H(6)BrFO(3), are essentially coplanar (r.m.s. deviation for all non-H atoms = 0.074 angstrom). In the crystal, the molecules are linked by C-H center dot center dot center dot O and C-H center dot center dot center dot Br interactions.

(1S*,3S*,8S*,10S*)-10-Fluoro-15-oxatetracyclo[6.6.1.0(1,10).0( 3,8)]pentadeca-5,12-dien-3-ol

The title compound, C(14)H(17)FO(2), was obtained from anti-4a, 9a:8a,10a-diepoxy-1,4,4a,5,8,8a, 9,9a, 10,10a-decahydroanthracene via tandem hydrogen-fluoride-mediated epoxide ring-opening and transannular oxacyclization. With the two cyclohexene rings folded towards the oxygen bridge, the title tetracyclic fluoroalcohol molecule displays a conformation reminiscent of a pagoda. The crystal packing is effected via intermolecular O-H center dot center dot center dot O hydrogen bonds, which link the molecules into a zigzag chain along the b axis.

N-(2-Amino-3,5-dibromobenzyl)-N-methylcyclohexan-1-aminium p-toluenesulfonate

The title compound, C(14)H(21)Br(2)N(2)(+)center dot C(7)H(7)O(3)S, features a salt of protonated bromhexine, a pharmaceutical used in the treatment of respiratory disorders, and the p-toluenesulfonate anion. The crystal packing is stabilized by intermolecular N-H center dot center dot center dot O, N-H center dot center dot center dot Br and C-H center dot center dot center dot O hydrogen bonds.

(2E)-1-(5-Chlorothiophen-2-yl)-3-(2,4,5-trimethoxyphenyl)prop-2-en-1-one

In the title molecule, C(16)H(15)ClO(4)S, the chlorothiophene and trimethoxyphenyl rings make a dihedral angle of 31.12 (5)degrees. The C = C double bond exhibits an E conformation. In the crystal, C-H center dot center dot center dot O interactions generate bifurcated bonds, linking the molecules into chains along the b axis.

4-(4-Chlorophenyl)-N-[(E)-4-(dimethylamino)benzylidene]-1,3-thiazol-2- amine

The title compound, C(18)H(16)ClN(3)S, adopts an extended molecular structure. The thiazole ring is inclined by 9.2 (1) and 15.3 (1)degrees with respect to the chlorophenyl and 4-(dimethylamino)phenyl rings, respectively, while the benzene ring planes make an angle of 19.0 (1)degrees. A weak intermolecular C-H center dot center dot center dot pi contact is observed in the crystal structure.

3-Ethyl-4-methyl-1H-pyrazol-2-ium-5-olate

The title compound, C(6)H(10)N(2)O, is a zwitterionic pyrazole derivative. The crystal packing is predominantly governed by a three-center iminium-amine N(+)-H center dot center dot center dot O(-)center dot center dot center dot H-N interaction, leading to an undulating sheet-like structure lying parallel to (100).

2-{[{2-Hydroxy-3-[2-methyl-5-(propan-2-yl)phenoxy]propyl}(pyridin -2-ylmethyl)amino]methyl}phenol

In the title racemic compound, C(26)H(32)N(2)O(3), an intramolecular O-H center dot center dot center dot N hydrogen bond is formed between the phenolic OH group and the tertiary amine N atom. Another O-H center dot center dot center dot N hydrogen bond that is formed between the OH group and the pyridine N atom links the molecules into a polymeric chain extending along the a axis. The structure is further stabilized by intramolecular and intermolecular C-H center dot center dot center dot O interactions.

Weak C-H center dot center dot center dot O hydrogen bonds in anisaldehyde, salicylaldehyde and cinnamaldehyde

In situ cryocrystallization has been employed to grow single crystals of 4-methoxybenzaldehyde (anisaldehyde), C(8)H(8)O(2), 2-hydroxybenzaldehyde (salicylaldehyde), C(7)H(6)O(2), and (2E)-3-phenylprop-2-enal (cinnamaldehyde), C(9)H(8)O, all of which are liquids at room temperature. Several weak C-H center dot center dot center dot O interactions of the types C(aryl)-H center dot center dot center dot O, C(formyl)-H center dot center dot center dot O and Csp(3)-H center dot center dot center dot O are present in these related crystal structures.

(2E)-1-(5-Chlorothiophen-2-yl)-3-(2,3-dimethoxyphenyl)prop-2-en-1-one

In the title compound, C(15)H(13)ClO(3)S, the chlorothiophene and dimethoxyphenyl groups are linked by a prop-2-en-1-one group. The C=C double bond exhibits an E conformation. The molecule is non-planar, with a dihedral angle of 31.12 (5)degrees between the chlorothiophene and dimethoxyphenyl rings. The methoxy group at position 3 is coplanar with the benzene ring to which it is attached, with a C-O-C-C torsion angle of -3.8 (3)degrees. The methoxy group attached at position 2 of the benzene ring is in a (+)synclinal conformation, as indicated by the C-O-C-C torsion angle of -73.6 (2)degrees. In the crystal, two different C-H center dot center dot center dot O intermolecular interactions generate chains of molecules extending along the b axis.

Methyl 2,2-bis(2,4-dinitrophenyl)ethanoate

In the title compound, C(15)H(10)N(4)O(10), the dihedral angle between the aromatic rings is 89.05 (16)degrees. One O atom of one of the nitro groups is disordered over two sites in a 0.70:0.30 ratio. In the crystal, the molecules are linked by weak C-H center dot center dot center dot O interactions.