Iodine in PDB 1wcb: Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten

The structure of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten, PDB code: 1wcb was solved by B.Golinelli-Pimpaneau, P.Christen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.900, 60.300, 64.600, 79.40, 78.20, 80.80
R / Rfree (%)	22.3 / 29

The binding sites of Iodine atom in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten (pdb code 1wcb). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten, PDB code: 1wcb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten within 5.0Å range: probe atom residue distance (Å) B Occ B:I1227 b:35.5 occ:1.00 NZ B:LYS96 3.5 26.3 1.0 O B:HOH2070 3.7 26.5 1.0 CE B:LYS96 3.9 26.3 1.0 C4A A:PE11215 4.0 15.3 1.0 CH2 B:TRP100E 4.1 9.4 1.0 CZ3 B:TRP100E 4.1 10.0 1.0 CB A:PE11215 4.4 16.5 1.0 CG A:PE11215 4.5 19.0 1.0 C4 A:PE11215 4.6 15.8 1.0 CD B:LYS96 4.6 24.8 1.0 O B:HOH2014 4.6 8.2 1.0 C5A A:PE11215 4.8 15.0 1.0 C5 A:PE11215 4.9 14.7 1.0 O4P A:PE11215 4.9 15.4 1.0

Iodine binding site 2 out of 9 in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten within 5.0Å range: probe atom residue distance (Å) B Occ B:I1228 b:17.1 occ:1.00 O B:HOH2067 3.3 14.4 1.0 ND2 B:ASN100A 3.3 22.9 1.0 CD1 B:TYR99 3.4 38.4 1.0 CA B:GLY97 3.4 18.4 1.0 C B:GLY97 3.6 20.2 1.0 NE1 B:TRP100E 3.6 11.5 1.0 N B:GLY97 3.7 16.7 1.0 CB B:ASN100A 3.7 25.9 1.0 O B:HOH2028 3.7 11.0 1.0 CB B:TYR99 3.8 34.0 1.0 N B:TYR99 3.8 31.4 1.0 O B:GLY97 3.9 17.9 1.0 CG B:ASN100A 3.9 24.3 1.0 N B:ASN100A 4.0 29.9 1.0 CG B:TYR99 4.0 37.0 1.0 N B:SER98 4.1 23.7 1.0 CA B:TYR99 4.2 33.1 1.0 C B:TYR99 4.3 33.6 1.0 CA B:ASN100A 4.4 28.5 1.0 CE1 B:TYR99 4.4 40.4 1.0 CE2 B:TYR32 4.4 12.3 1.0 CD1 B:TRP100E 4.6 11.2 1.0 CE2 B:TRP100E 4.6 9.4 1.0 N B:GLY100 4.6 32.9 1.0 C B:SER98 4.7 29.3 1.0 O B:TYR99 4.7 34.7 1.0 CZ2 B:TRP100E 4.8 10.7 1.0 C B:LYS96 4.9 16.6 1.0 C B:ASN100A 4.9 29.5 1.0 OD1 B:ASN100A 5.0 23.7 1.0

Iodine binding site 3 out of 9 in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten within 5.0Å range: probe atom residue distance (Å) B Occ B:I1229 b:53.2 occ:1.00 N B:ARG71 3.6 7.5 1.0 NZ B:LYS57 3.9 33.9 1.0 CA B:SER70 4.0 8.6 1.0 CB B:SER70 4.0 6.0 1.0 CG B:ARG71 4.0 9.7 1.0 O B:ARG71 4.0 8.7 1.0 CD1 B:ILE51 4.1 7.9 1.0 C B:SER70 4.3 8.1 1.0 CE B:LYS57 4.3 30.6 1.0 CA B:ARG71 4.6 8.8 1.0 C B:ARG71 4.8 8.7 1.0 CB B:ARG71 4.9 6.5 1.0

Iodine binding site 4 out of 9 in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten within 5.0Å range: probe atom residue distance (Å) B Occ B:I1230 b:78.8 occ:1.00 O B:HOH2047 3.4 8.6 1.0 OG1 B:THR68 3.9 17.6 1.0 ND2 B:ASN82A 4.8 22.4 1.0

Iodine binding site 5 out of 9 in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten within 5.0Å range: probe atom residue distance (Å) B Occ H:I1213 b:49.5 occ:1.00 NE1 H:TRP100E 3.5 19.4 1.0 CD1 H:TYR99 3.5 49.2 1.0 CA H:GLY97 3.6 29.4 1.0 CB H:ASN100A 3.7 35.8 1.0 N H:TYR99 3.7 43.2 1.0 CB H:TYR99 3.8 45.4 1.0 N H:GLY97 3.8 26.6 1.0 N H:ASN100A 3.9 37.0 1.0 C H:GLY97 3.9 32.7 1.0 C H:TYR99 4.0 43.1 1.0 CA H:TYR99 4.0 43.9 1.0 O H:TYR99 4.0 43.9 1.0 ND2 H:ASN100A 4.1 39.1 1.0 CG H:TYR99 4.1 48.3 1.0 CA H:ASN100A 4.2 35.5 1.0 CE2 H:TYR32 4.2 25.6 1.0 N H:SER98 4.3 35.3 1.0 CG H:ASN100A 4.3 37.1 1.0 O H:GLY97 4.3 32.8 1.0 CD1 H:TRP100E 4.4 19.6 1.0 CE2 H:TRP100E 4.4 19.5 1.0 O H:ASN100A 4.5 32.7 1.0 N H:GLY100 4.5 41.1 1.0 C H:ASN100A 4.5 33.6 1.0 OH H:TYR32 4.6 26.5 1.0 CE1 H:TYR99 4.6 50.8 1.0 CZ2 H:TRP100E 4.6 21.0 1.0 CZ H:TYR32 4.8 25.6 1.0 C H:SER98 4.9 41.2 1.0 C H:GLY100 5.0 38.6 1.0

Iodine binding site 6 out of 9 in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten within 5.0Å range: probe atom residue distance (Å) B Occ H:I1214 b:84.3 occ:1.00 N H:ALA84 3.5 22.0 1.0 CB H:ALA84 4.0 19.9 1.0 CB H:PRO14 4.0 14.8 1.0 CA H:ARG83 4.1 21.7 1.0 CB H:ARG83 4.2 20.4 1.0 C H:ARG83 4.3 22.6 1.0 CA H:ALA84 4.3 19.8 1.0 CG H:PRO14 4.4 17.2 1.0

Iodine binding site 7 out of 9 in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten within 5.0Å range: probe atom residue distance (Å) B Occ H:I1215 b:67.0 occ:1.00 N H:ARG71 3.4 8.3 1.0 CB H:SER70 3.7 7.1 1.0 CA H:SER70 3.7 7.2 1.0 O H:ARG71 3.9 11.9 1.0 NZ H:LYS57 4.0 27.8 1.0 CD1 H:ILE51 4.1 1.0 1.0 C H:SER70 4.1 7.3 1.0 CG H:ARG71 4.3 12.8 1.0 CE H:LYS57 4.5 24.6 1.0 CA H:ARG71 4.5 10.7 1.0 C H:ARG71 4.7 11.5 1.0 OG H:SER70 5.0 9.3 1.0 O H:ILE69 5.0 9.7 1.0 CB H:ARG71 5.0 10.9 1.0

Iodine binding site 8 out of 9 in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten within 5.0Å range: probe atom residue distance (Å) B Occ H:I1216 b:28.7 occ:1.00 NZ H:LYS96 3.4 28.5 1.0 C4A L:PE11216 4.0 13.5 1.0 CE H:LYS96 4.0 26.7 1.0 CB L:PE11216 4.2 16.7 1.0 CZ3 H:TRP100E 4.4 20.8 1.0 CH2 H:TRP100E 4.4 19.1 1.0 CG L:PE11216 4.6 18.9 1.0 C4 L:PE11216 4.6 13.6 1.0 C5A L:PE11216 4.8 14.4 1.0 CD H:LYS96 4.9 26.5 1.0

Iodine binding site 9 out of 9 in the Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Plp-Dependent Catalytic Antibody 15A9 in Complex with Its Hapten within 5.0Å range: probe atom residue distance (Å) B Occ L:I1215 b:53.5 occ:1.00 OG L:SER191 3.3 26.8 1.0 N B:GLU85 3.7 15.9 1.0 ND2 L:ASN210 3.9 46.4 1.0 CB B:GLU85 3.9 17.8 1.0 CB L:SER191 4.0 27.5 1.0 CG B:GLU85 4.0 19.5 1.0 O L:PHE209 4.0 48.8 1.0 CB B:ARG83 4.0 19.2 1.0 OG L:SER208 4.1 44.4 1.0 CB L:ASN210 4.1 49.4 1.0 N B:ALA84 4.2 18.4 1.0 CB B:ALA84 4.2 17.6 1.0 O B:HOH2065 4.3 27.6 1.0 CA B:GLU85 4.4 16.9 1.0 CA L:SER191 4.5 29.6 1.0 C L:PHE209 4.5 48.7 1.0 CG L:ASN210 4.5 48.1 1.0 CA B:ALA84 4.6 17.3 1.0 CB L:SER208 4.6 45.4 1.0 C B:ALA84 4.6 17.3 1.0 CD B:ARG83 4.6 24.8 1.0 CA L:ASN210 4.8 51.0 1.0 C B:ARG83 4.9 18.3 1.0 CG B:ARG83 4.9 22.6 1.0 N L:ASN210 4.9 49.6 1.0

B.Golinelli-Pimpaneau, C.Luthi, P.Christen. Structural Basis For D-Amino Acid Transamination By the Pyridoxal- 5' -Phosphate - Dependent Catalytic Antibody 15A9. J.Biol.Chem. V. 281 23969 2006.
ISSN: ISSN 0021-9258
PubMed: 16790434
DOI: 10.1074/JBC.M602184200