Non-member submission forwarded by the list-ownerHi,
--------------------------------------------------------------------------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
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
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