Modeller Care wrote:
> Non-member submission forwarded by the list-owner > -------------------------------------------------------------------------- > > I would like to model a protein that contains Zn in the active site. In = > the template structure, two His residues are coordinated to the Zn. The = > target sequence also has these residues and the sequences display > 50% = > identity. How do I force the His residues to similarly coordinate the = > Zn in the modelled structure? If the Zn atom is in .pdb file, modeller = > doesn't seem to notice. Without the Zn atom present, the His = > sidechains simply flop around in the active site (not surprisingly). > > Marc Campitelli
Hi, sounds familiar... You need to:
i) put in the top file: SET HETATM_IO = on
ii)put in the end of the alignment that you will use to make the model (ali file):
/z/*
Note: I put the symbol z that describe Zn2+, but you have to take a look in the modlib directory. The file name is restyp.lib taht look like this:
# PDB-3 PDB-1 CHARMM DESCRIPTION #-----------------------------------------------------------------------------
1 | ALA | A | ALA | alanine 2 | CYS CYS CSH | C | CYS | cysteine 3 | ASP | D | ASP | aspartic acid, +1 4 | GLU | E | GLU | glutamic acid, +1 5 | PHE | F | PHE | phenylalanine 6 | GLY | G | GLY | glycine 7 | HIS | H | HSD | histidine, neutral, proton on ND1 8 | ILE | I | ILE | isoleucine 9 | LYS | K | LYS | lysine, +1 10 | LEU | L | LEU | leucine 11 | MET | M | MET | methionine 12 | ASN | N | ASN | asparagine 13 | PRO PR0 PRZ | P | PRO | proline 14 | GLN | Q | GLN | glutamine 15 | ARG | R | ARG | arginine, +1 16 | SER | S | SER | serine 17 | THR | T | THR | threonine 18 | VAL | V | VAL | valine 19 | TRP | W | TRP | tryptophan 20 | TYR | Y | TYR | tryrosine 21 | GAP | - | GAP | an alignment gap 22 | ASX | B | ASX | ASP/ASN ambiguous 23 | GLX | Z | GLX | GLU/GLN ambiguous 24 | UNK | X | UNK | unknown residue type 25 | PCA PGA | p | #### | pyrrolidine carboxylic acid (pyroglutamate) 26 | HSE | 6 | HSE | histidine, neutral, proton on NE2 27 | HSP | 7 | HSP | histidine, +1 (proton on NE2 and ND1) 28 | HOH H2O OH2 MOH WAT | w | TIP3 | water 29 | CAL CA | 3 | CAL | calcium ion, +2 30 | ZN2 | z | ZN2 | zinc, +2 31 | HEM | h | HEME | heme ligand 32 | NTR | n | NTER | patch for standard N-terminus, +1 33 | GLP | # | GLYP | patch for glycine N-terminus 34 | PRP | # | PROP | patch for proline N-terminus 35 | ACE | e | ACE | patch for acetylated N-terminus 36 | TER | c | CTER | patch for standard C-terminus 37 | CT1 | # | CT1 | patch for methylated C-terminus from methyl acetate 38 | CT2 | # | CT2 | patch for amidated C-terminus 39 | CT3 | # | CT3 | patch for N-Methylamide C-terminus 40 | ASP | # | ASPP | protonated aspartate, proton on OD2 41 | GLU | # | GLUP | protonated glutamate, proton on OE2 42 | LNK | # | LINK | patch for linkage of images or segments 43 | DIS | # | DISU | patch for disulfide 44 | HS2 | # | HS2 | patch for neutr His, + from ND1 to NE2
45 | O2 | # | O2 | O2 ligand for heme 46 | CO | # | CO | CO ligand for heme 47 | FHM | # | FHEM | patch for heme 48 | PHM | # | PHEM | patch for heme 49 | PLO | # | PLO2 | patch for heme 50 | LIG | # | PLIG | patch for heme 51 | LWA | # | PLWA | patch for heme 52 | CYS CSS CYX | C | CSS | cystine 53 | ABU | g | #### | amino-butyric acid 54 | ACD | d | #### | acidic unknown 55 | ALB | l | #### | beta-alanine 56 | ALI | a | #### | aliphatic unknown 57 | ARO | r | #### | aromatic unknown 58 | BAS | b | #### | basic unknown 59 | HYP | # | #### | hydroxyproline 60 | SAR | s | #### | sarcosine 61 | FOR | f | #### | formyl 62 | MSE | M | #### | selenomethionine 63 | MEX | C | #### | cysteine bridged with beta-mercaptoethanol 64 | SO4 | # | SO4 | sulphate ion -2 65 | ABU | # | #### | similar to Cys, but SG->CG 66 | ACP | # | ACP | acetylated N-terminus for proline 67 | BRK | / | BRK | chain break 68 | HIS | H | HIS | histidine for TOPH19 69 | HIS | H | HSC | doubly protonated HIS for TOPH19 70 | PEN | # | PEN | Penicillamine for TOPH19 71 | FRM | # | FORM | for TOPH19 72 | AMN | # | AMN | for TOPH19 73 | CBX | # | CBX | for TOPH19 74 | ETH | # | ETH | for TOPH19 75 | OHH | # | OH2 | TIPS3P water model for TOPH19 76 | COH | # | COH | for TOPH19 77 | ST2 | # | ST2 | for TOPH19 78 | LTD | # | LTOD | patch for TOPH19 79 | LG1 | # | LIG1 | cyclic patch 80 | LG2 | # | LIG2 | cyclic patch 81 | LG3 | # | LIG3 | cyclic patch 82 | BLK | . | BLK | BLOCK, place holder 83 | 5PH | # | 5PHO | 5'terminal PHOSPHATE patch 84 | 3TE | # | 3TER | 3'terminal HYDROXYL patch, from MeOH 85 | 3PH | # | 3PHO | 3'terminal PHOSPHATE patch 86 | 9MG | # | 9MG | 9-Methyl guanine patch 87 | 9EG | # | 9EG | 9-Ethyl guanine patch 88 | 9MA | # | 9MA | 9-Methyl adenine patch 89 | 1MC | # | 1MC | 1-Methyl Cytosine patch 90 | 1MT | # | 1MT | 1-Methyl Thymine patch 91 | NAG | 1 | NAG | N-ACETYL-D-GLUCOSAMINE 92 | MAN | 2 | MAN | ALPHA-D-MANNOSE 93 | MN | 4 | MN | manganese ion, +2 94 | MYR | 5 | MYR | MYRISTATE 95 | GDP | x | GDP | GDP 96 | GTP | y | GTP | GTP 97 | LN2 | # | LNK2 | NH3 Lys - CONH Gln (sc to sc) link patch 98 | LN3 | # | LNK3 | CO to NH3 Lys (backb to sdch) link patch 99 | LN4 | # | LNK4 | COOH to NH sdch to backb link patch 100 | IGL | q | IGLN | iso-glutamin 101 | 156 | i | 0156 | 0156 102 | ATP | @ | ATP | ATP 103 | MG | $ | MG | magnesium ion 104 | K | % | K | potassium ion 105 | 25P | # | 25P1 | patch to convert a 3'-5' phosphodiester 106 | 25P | # | 25P2 | patch to convert a 3'-5' phosphodiester 107 | 5DP | # | 5DP | patch to create 5' diphosphate on nucleotides, jjp1/adm jr. 108 | 5MC | # | 5MC1 | Patch to generate 5-methylcytosine (base only) 109 | 5MC | # | 5MC2 | Patch to convert cytosine to 5-methylcytosine 110 | 5ME | # | 5MET | 5'-ribose METHYL patch 111 | 5TE | # | 5TER | 5'-terminal HYDROXYL patch, from MeOH 112 | ADE | # | ADE | 113 | ADP | # | ADP | adenosine diphosphate, jjp1/adm jr. 114 | CYT | # | CYT | 115 | DEO | # | DEO1 | Patch to make DEOXYribose in PYRIMIDINES 116 | DEO | # | DEO2 | Patch to make DEOXYribose in PURINES 117 | DEO | # | DEOT | DEOXYRIBOSE, Wilma Olsen's dihedral model 118 | DMP | # | DMPA | Dimethylphosphate 119 | DUM | # | DUM | DUMMY ATOM 120 | GUA | # | GUA | 121 | INO | # | INO1 | patch to convert guanine to inosine 122 | MP_ | # | MP_0 | Methylphosphate, neutral 123 | MP_ | # | MP_1 | Methylphosphate, anionic 124 | MP_ | # | MP_2 | Methylphosphate, dianionic 125 | NAD | # | NAD | oxidized nicotinamide adenine dinucleotide, jjp1/adm jr. 126 | NAD | # | NADH | reduced nicotinamide adenine dinucleotide, jjp1/adm jr. 127 | NIC | # | NIC | oxidized nicotinamide, jjp1/adm jr. 128 | NIC | # | NICH | reduced nicotinamide, jjp1/adm jr. 129 | PPI | # | PPI1 | Inorganic phosphate, jjp1/adm jr. 130 | PUR | # | PURA | Patch to generate ADENINE (purine) 131 | PUR | # | PURG | Patch to generate GUANINE (purine) 132 | PYR | # | PYRC | Patch to generate CYTOSINE (pyrimidine) 133 | PYR | # | PYRU | Patch to generate URACIL or THYMINE (pyrimidine) 134 | RIB | # | RIBT | RIBOSE, Wilma Olsen's dihedral model 135 | SOD | # | SOD | Sodium Ion 136 | THY | # | THY | 137 | TP1 | # | TP1 | convert tyrosine to monoanionic phosphotyrosine 138 | TP1 | # | TP1A | patch to convert tyrosine to 139 | TP2 | # | TP2 | patch to convert tyrosine to 140 | TP2 | # | TP2A | patch to convert tyrosine to 141 | URA | # | URA |
iii) edit the template.pdb like
TER ATOM natom MG MG nres x y z
You can force the His to be in the same coordinate using:
http://salilab.org/modeller/manual/node68.html
Hope it helps
Luca
-------------------------------------------------------- Luca Settimo, Ph.D. Student
Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University Tykistökatu 6A 20520 Turku Finland phone: +358-2-215-4600 fax: +358-2-2153280 mailto:lsettimo@abo.fi Webpage URL http://www.abo.fi/~lsettimo --------------------------------------------------------