AV - CCP4

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Transcript AV - CCP4

Crystal structure description
crystal
Asym.part
chain
monomer
atom
Dictionary
Description of
Monomers
atoms
Links
modifications
Atomic model description in PDB
Default pointers in PDB file
. . . . . .
ATOM
7
ATOM
8
ATOM
9
ATOM
10
ATOM
11
. . . . . .
C
O
N
CA
CB
LEU
LEU
ILE
ILE
ILE
A
A
A
A
A
5
5
6
6
6
37.584
36.548
37.887
37.032
37.835
Pointer to link description
Pointer to monomer description
Pointer to atom description
4.085
3.447
5.098
5.447
6.276
Refmac Dictionary
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Describes all amino acids
All nucleic acids
Common sugars
Many organic and inorganic compounds
Links and modifications
There are tools to deal with dictionary
Dictionary format is mmCIF
dictionary
list of monomers
list of links
list of modifications
list of
atom types
atoms
bonds
atoms
types
bonds
angles
bonds
bonds
angles
torsions
angles
angles
torsions
chiralities
torsions
VDW
chiralities
planes
chiralities
H-bonds
planes
tree
planes
tree
tree
Example of peptide link
O
+
NH3
O
H R1 H
H R2
H R1
+
O
+
NH3
O
+
NH3
H2O
O
N
O
O R2 H
Link formalism allows to join monomers together
Link describes in details the result of chemical reaction
Example of a modification
2O
H
O
O
+
NH3
+
O
P
3-
CH2OH
O
O
P
O
O
H
O
-
OH
O
CH2
O
+
NH3
O
Modification formalism allows to change a monomer
Modification describes in details the result of chemical
reaction
Thank you very much