Iodine in PDB 6k60: Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs

The structure of Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs, PDB code: 6k60 was solved by K.Kuroki, H.Matsubara, R.Kanda, N.Miyashita, M.Shiroishi, Y.Fukunaga, J.Kamishikiryo, A.Fukunaga, K.Hirose, Y.Sugita, S.Kita, T.Ose, K.Maenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.81 / 3.15
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	164.378, 164.378, 326.839, 90.00, 90.00, 120.00
R / Rfree (%)	26.1 / 28.9

The binding sites of Iodine atom in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs (pdb code 6k60). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs, PDB code: 6k60:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:79.2 occ:1.00 NH1 A:ARG75 3.9 63.4 1.0 CB A:PRO43 4.1 66.5 1.0 NH2 A:ARG75 4.2 59.0 1.0 CZ A:PHE36 4.3 65.3 1.0 CB A:SER38 4.3 57.8 1.0 CZ A:ARG75 4.4 60.1 1.0 CG A:PRO43 4.5 66.2 1.0 CB A:ALA71 4.5 56.0 1.0 CA A:SER38 4.6 56.8 1.0 CE1 A:PHE36 4.7 60.7 1.0 CG A:LYS68 5.0 67.1 1.0

Iodine binding site 2 out of 8 in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:82.8 occ:1.00 CA A:GLY175 4.1 92.6 1.0 CB A:GLU177 4.1 99.6 1.0 CD1 A:TRP51 4.2 87.3 1.0 CB A:MET178 4.2 92.8 1.0 N A:MET178 4.2 93.7 1.0 C A:GLY175 4.4 87.3 1.0 CA F:GLY18 4.4 78.8 1.0 N F:GLY18 4.5 78.8 1.0 O A:GLY175 4.5 82.8 1.0 O A:ASN174 4.5 95.2 1.0 N A:GLU177 4.6 91.4 1.0 CE A:MET178 4.7 0.5 1.0 CB A:TRP51 4.8 89.0 1.0 CA A:GLU177 4.8 92.1 1.0 CG A:TRP51 4.9 86.1 1.0 CA A:MET178 4.9 88.7 1.0 C A:GLU177 4.9 87.4 1.0

Iodine binding site 3 out of 8 in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs within 5.0Å range: probe atom residue distance (Å) B Occ B:I1000 b:0.5 occ:1.00 N B:GLY43 3.4 61.5 1.0 CB B:ALA79 3.5 69.4 1.0 O B:GLU77 3.6 66.4 1.0 N B:ASN42 3.9 61.7 1.0 CA B:ASN42 4.0 65.5 1.0 C B:GLU77 4.1 68.6 1.0 C B:ASN42 4.1 67.4 1.0 N B:ALA79 4.1 63.9 1.0 C B:TYR78 4.2 67.8 1.0 CA B:GLY43 4.2 65.1 1.0 CB B:GLU77 4.2 78.0 1.0 O B:TYR78 4.4 71.8 1.0 CA B:ALA79 4.4 64.2 1.0 N B:TYR78 4.5 72.8 1.0 O B:LEU40 4.5 57.5 1.0 CA B:TYR78 4.5 67.4 1.0 CB B:LEU40 4.5 60.4 1.0 C B:LYS41 4.8 64.0 1.0 C B:LEU40 4.8 56.5 1.0 OE1 B:GLU77 4.8 86.5 1.0 CA B:GLU77 4.8 73.7 1.0

Iodine binding site 4 out of 8 in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs within 5.0Å range: probe atom residue distance (Å) B Occ C:I101 b:98.6 occ:1.00 CG C:PRO4 3.9 72.8 1.0 CG1 C:ILE3 3.9 69.7 1.0 CB C:ARG5 3.9 74.7 1.0 N C:ARG5 4.1 71.7 1.0 NH1 A:ARG156 4.1 66.8 1.0 CD1 C:ILE3 4.2 66.0 1.0 CD C:PRO4 4.2 70.8 1.0 CG C:ARG5 4.2 75.2 1.0 CB A:GLN155 4.3 80.9 1.0 CA C:ARG5 4.5 71.5 1.0 N C:PRO4 4.6 69.2 1.0 CD A:GLN155 4.7 78.0 1.0 OE1 A:GLN155 4.7 75.8 1.0 O C:ARG5 4.7 64.8 1.0 O A:GLN155 4.8 86.4 1.0 CB C:PRO4 4.9 72.3 1.0 CG A:GLN155 4.9 80.5 1.0 C C:PRO4 4.9 69.6 1.0

Iodine binding site 5 out of 8 in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs within 5.0Å range: probe atom residue distance (Å) B Occ E:I301 b:79.0 occ:1.00 CA E:GLY175 4.0 69.7 1.0 CB E:MET178 4.1 71.1 1.0 CD1 E:TRP51 4.1 73.4 1.0 N E:MET178 4.3 74.5 1.0 CA B:GLY18 4.4 71.1 1.0 C E:GLY175 4.4 69.8 1.0 O E:GLY175 4.4 69.3 1.0 CE E:MET178 4.5 69.2 1.0 CB E:TRP51 4.5 70.2 1.0 N B:GLY18 4.6 65.9 1.0 CB E:GLU177 4.7 76.7 1.0 O E:ASN174 4.7 73.1 1.0 CG E:TRP51 4.7 70.4 1.0 CA E:MET178 4.8 73.1 1.0 N E:TRP51 4.9 72.5 1.0 N E:GLU177 4.9 75.5 1.0 CB E:PRO50 5.0 80.4 1.0

Iodine binding site 6 out of 8 in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs within 5.0Å range: probe atom residue distance (Å) B Occ E:I302 b:87.0 occ:1.00 NH2 E:ARG75 3.6 64.5 1.0 CB E:SER38 4.0 64.6 1.0 CZ E:PHE36 4.1 71.3 1.0 CB E:PRO43 4.1 75.5 1.0 NH1 E:ARG75 4.1 70.0 1.0 CZ E:ARG75 4.2 66.0 1.0 CA E:SER38 4.4 70.2 1.0 CB E:ALA71 4.4 60.1 1.0 CG E:PRO43 4.5 78.3 1.0 CE1 E:PHE36 4.6 70.2 1.0 O E:SER38 5.0 80.2 1.0 OE1 E:GLN72 5.0 70.7 1.0

Iodine binding site 7 out of 8 in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs within 5.0Å range: probe atom residue distance (Å) B Occ E:I303 b:0.7 occ:1.00 CB E:GLN141 3.7 61.4 1.0 CG E:GLN141 3.9 62.2 1.0 NZ E:LYS144 4.0 61.1 1.0 NE2 E:GLN141 4.0 64.8 1.0 CD E:LYS144 4.1 59.8 1.0 CD E:GLN141 4.1 64.0 1.0 CG E:ARG145 4.1 57.4 1.0 CA E:GLN141 4.2 60.0 1.0 CD E:ARG145 4.3 58.4 1.0 O E:GLN141 4.3 60.0 1.0 CE E:LYS144 4.4 60.4 1.0 C E:GLN141 4.7 59.8 1.0 OE1 E:GLN141 4.9 64.6 1.0 CG E:LYS144 4.9 59.4 1.0

Iodine binding site 8 out of 8 in the Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structural and Functional Basis For Hla-G Isoform Recognition of Immune Checkpoint Receptor Lilrbs within 5.0Å range: probe atom residue distance (Å) B Occ G:I1000 b:95.2 occ:1.00 CD G:PRO4 3.9 52.7 1.0 CB G:ARG5 3.9 63.5 1.0 N G:ARG5 3.9 59.9 1.0 NH1 E:ARG156 3.9 59.6 1.0 CG G:ARG5 4.0 62.8 1.0 CG1 G:ILE3 4.0 56.7 1.0 N G:PRO4 4.4 57.1 1.0 CG G:PRO4 4.5 52.9 1.0 CA G:ARG5 4.5 63.4 1.0 CD1 G:ILE3 4.5 58.0 1.0 CB G:PRO4 4.5 57.9 1.0 OE1 E:GLN155 4.7 70.3 1.0 CD E:GLN155 4.7 69.6 1.0 CB E:GLN155 4.7 67.7 1.0 NE2 E:GLN155 4.7 69.8 1.0 C G:PRO4 4.7 63.5 1.0 O G:ARG5 4.7 62.7 1.0 CA G:PRO4 4.8 59.8 1.0

K.Kuroki, H.Matsubara, R.Kanda, N.Miyashita, M.Shiroishi, Y.Fukunaga, J.Kamishikiryo, A.Fukunaga, H.Fukuhara, K.Hirose, J.S.Hunt, Y.Sugita, S.Kita, T.Ose, K.Maenaka. Structural and Functional Basis For Lilrb Immune Checkpoint Receptor Recognition of Hla-G Isoforms. J Immunol. 2019.
ISSN: ESSN 1550-6606
PubMed: 31694909
DOI: 10.4049/JIMMUNOL.1900562