Chlorine in PDB 8c7j: Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format

The structure of Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format, PDB code: 8c7j was solved by R.Adams, A.Macpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.94 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.24, 71.31, 125.89, 90, 90, 90
R / Rfree (%)	18.6 / 22.6

The binding sites of Chlorine atom in the Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format (pdb code 8c7j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format, PDB code: 8c7j:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:39.6 occ:1.00 H A:TYR33 2.5 37.5 1.0 HA A:ASN32 2.9 53.6 1.0 O A:HOH535 3.0 39.9 1.0 O A:HOH584 3.1 50.1 1.0 O A:HOH427 3.2 33.0 1.0 HB3 A:ASN32 3.2 56.7 1.0 HB2 A:ARG145 3.2 35.2 1.0 HD2 A:ARG145 3.3 43.0 1.0 N A:TYR33 3.3 31.1 1.0 OD1 A:ASN32 3.5 48.6 1.0 CA A:ASN32 3.6 44.6 1.0 HB2 A:TYR33 3.7 47.8 1.0 CB A:ASN32 3.7 47.2 1.0 HD1 A:TYR33 3.9 64.8 1.0 O A:HOH524 3.9 39.5 1.0 C A:ASN32 4.0 43.0 1.0 CG A:ASN32 4.1 52.9 1.0 HA A:SER148 4.1 45.5 1.0 CB A:ARG145 4.1 29.2 1.0 CD A:ARG145 4.2 35.8 1.0 HG3 A:ARG145 4.2 42.2 1.0 CD1 A:TYR33 4.2 53.9 1.0 H A:ARG145 4.3 40.1 1.0 CB A:TYR33 4.3 39.8 1.0 CA A:TYR33 4.3 37.4 1.0 CG A:ARG145 4.4 35.1 1.0 CG A:TYR33 4.4 43.7 1.0 HB3 A:ARG145 4.6 35.2 1.0 O A:ASP31 4.6 37.2 1.0 HB2 A:ASN32 4.6 56.7 1.0 O A:TYR33 4.6 37.2 1.0 N A:SER148 4.7 32.8 1.0 HD3 A:ARG145 4.7 43.0 1.0 H A:SER148 4.8 39.4 1.0 O A:HOH555 4.8 46.4 1.0 CA A:SER148 4.8 37.9 1.0 HE A:ARG145 4.9 45.3 1.0 C A:TYR147 4.9 35.0 1.0 HE2 A:HIS35 4.9 41.5 1.0 O A:HOH477 4.9 40.9 1.0 N A:ARG145 4.9 33.4 1.0 N A:ASN32 4.9 41.2 1.0 HB2 A:SER148 5.0 54.5 1.0 C A:TYR33 5.0 35.3 1.0 HB2 A:ARG144 5.0 41.8 1.0

Chlorine binding site 2 out of 5 in the Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:63.2 occ:1.00 H A:ALA134 2.4 51.7 1.0 HB3 A:PRO14 2.9 49.4 1.0 HB2 A:ALA134 3.2 50.6 1.0 N A:ALA134 3.2 43.0 1.0 HA A:ARG133 3.2 48.5 1.0 HG3 A:PRO14 3.3 53.3 1.0 HB2 A:ARG133 3.6 50.5 1.0 HB3 A:ARG133 3.7 50.5 1.0 CB A:PRO14 3.7 41.0 1.0 CB A:ALA134 3.8 42.1 1.0 HB3 A:ALA134 3.8 50.6 1.0 CA A:ARG133 3.8 40.3 1.0 CG A:PRO14 3.8 44.4 1.0 CB A:ARG133 3.9 42.0 1.0 HG2 A:PRO14 4.0 53.3 1.0 C A:ARG133 4.0 45.4 1.0 CA A:ALA134 4.0 44.3 1.0 HG13 A:VAL163 4.2 46.8 1.0 HB2 A:PRO14 4.3 49.4 1.0 HA A:ALA134 4.3 53.3 1.0 HA A:PRO14 4.5 48.1 1.0 HB1 A:ALA134 4.7 50.6 1.0 CA A:PRO14 4.7 40.0 1.0

Chlorine binding site 3 out of 5 in the Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:84.6 occ:1.00 HD2 A:PRO14 2.7 53.5 1.0 HB3 A:SER165 2.7 60.1 1.0 HB2 A:SER165 3.0 60.1 1.0 HD3 A:LYS13 3.0 79.5 1.0 CB A:SER165 3.2 50.0 1.0 HB3 A:LYS13 3.3 62.9 1.0 HA A:SER165 3.3 58.0 1.0 CD A:PRO14 3.6 44.5 1.0 HG2 A:PRO14 3.6 53.3 1.0 CA A:SER165 3.8 48.3 1.0 CD A:LYS13 4.0 66.2 1.0 CG A:PRO14 4.1 44.4 1.0 HD3 A:PRO14 4.1 53.5 1.0 HB2 A:PRO14 4.2 49.4 1.0 CB A:LYS13 4.2 52.3 1.0 HZ3 A:LYS13 4.2 71.4 1.0 HD2 A:LYS13 4.3 79.5 1.0 N A:PRO14 4.4 43.6 1.0 OG A:SER165 4.5 58.7 1.0 CG A:LYS13 4.5 54.7 1.0 HG A:SER165 4.5 70.5 1.0 HG2 A:LYS13 4.6 65.8 1.0 N A:SER165 4.6 40.7 1.0 CB A:PRO14 4.6 41.0 1.0 HA A:LYS13 4.7 49.4 1.0 NZ A:LYS13 4.8 59.5 1.0 HB2 A:LYS13 4.8 62.9 1.0 H A:SER165 4.8 49.0 1.0 HZ1 A:LYS13 4.9 71.4 1.0 CA A:LYS13 4.9 41.1 1.0 O A:PRO14 5.0 45.4 1.0 CE A:LYS13 5.0 68.5 1.0 HG3 A:PRO14 5.0 53.3 1.0 C A:SER165 5.0 41.6 1.0

Chlorine binding site 4 out of 5 in the Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:48.2 occ:1.00 HH A:TYR197 2.2 40.3 1.0 H A:VAL202 2.5 37.5 1.0 HA A:PRO201 2.6 38.6 1.0 OH A:TYR197 2.9 33.5 1.0 HG22 A:VAL202 3.1 47.2 1.0 O A:HOH563 3.1 42.8 1.0 HG2 A:GLU200 3.1 41.5 1.0 OE2 A:GLU200 3.2 48.5 1.0 HB3 A:ALA220 3.2 40.7 1.0 HB3 A:GLU200 3.2 36.3 1.0 HE2 A:TYR197 3.3 33.0 1.0 N A:VAL202 3.3 31.1 1.0 CA A:PRO201 3.5 32.1 1.0 HD22 A:LEU230 3.6 48.7 1.0 HA A:GLU200 3.7 34.3 1.0 CG A:GLU200 3.7 34.5 1.0 HB1 A:ALA220 3.8 40.7 1.0 CZ A:TYR197 3.8 33.1 1.0 CB A:GLU200 3.8 30.1 1.0 C A:PRO201 3.8 32.1 1.0 CD A:GLU200 3.9 49.0 1.0 CE2 A:TYR197 3.9 27.4 1.0 HB2 A:PRO201 3.9 37.4 1.0 CB A:ALA220 3.9 33.8 1.0 HB3 A:PRO201 4.0 37.4 1.0 CG2 A:VAL202 4.0 39.2 1.0 CB A:PRO201 4.0 31.1 1.0 O A:VAL202 4.2 30.4 1.0 CA A:GLU200 4.2 28.5 1.0 HD23 A:LEU230 4.3 48.7 1.0 HB2 A:ALA220 4.4 40.7 1.0 CD2 A:LEU230 4.4 40.5 1.0 CA A:VAL202 4.4 30.7 1.0 HG13 A:VAL202 4.4 42.8 1.0 HG23 A:VAL202 4.5 47.2 1.0 HG21 A:VAL202 4.5 47.2 1.0 H A:ALA220 4.6 37.4 1.0 HG3 A:GLU200 4.6 41.5 1.0 N A:PRO201 4.6 29.4 1.0 CB A:VAL202 4.7 34.1 1.0 HB2 A:GLU200 4.7 36.3 1.0 HD21 A:LEU230 4.8 48.7 1.0 C A:VAL202 4.8 33.0 1.0 OE1 A:GLU200 5.0 48.5 1.0

Chlorine binding site 5 out of 5 in the Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Phage Display Derived Serum Albumin Binding Knob Domain Engineered Within A Novel Vh Framework 3 Bispecific Antibody Format within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:38.4 occ:1.00 H B:ASP50 2.4 35.2 1.0 HD21 B:ASN91 2.8 55.4 1.0 O B:HOH540 2.9 48.2 1.0 HB2 B:ASN91 3.1 56.9 1.0 HG3 A:PRO151 3.2 47.2 1.0 O B:HOH550 3.2 36.2 1.0 N B:ASP50 3.3 29.3 1.0 HB2 B:TYR49 3.3 34.2 1.0 HB1 B:ALA34 3.5 39.3 1.0 ND2 B:ASN91 3.5 46.1 1.0 HA2 B:GLY32 3.6 40.1 1.0 HA B:ASP50 3.6 32.4 1.0 H B:LEU33 3.6 40.8 1.0 N B:LEU33 3.6 33.9 1.0 C B:LEU33 3.7 33.8 1.0 O A:HOH574 3.7 49.9 1.0 HA B:TYR49 3.7 32.6 1.0 C B:GLY32 3.7 34.7 1.0 O B:LEU33 3.7 31.5 1.0 OD1 B:ASP50 3.8 34.4 1.0 CB B:ASN91 3.9 47.4 1.0 CA B:ASP50 4.0 26.9 1.0 HD22 B:ASN91 4.0 55.4 1.0 N B:ALA34 4.0 28.5 1.0 CB B:TYR49 4.0 28.4 1.0 CG A:PRO151 4.1 39.3 1.0 CA B:LEU33 4.1 35.8 1.0 CG B:ASN91 4.1 46.5 1.0 CA B:GLY32 4.1 33.3 1.0 CA B:TYR49 4.2 27.1 1.0 O B:GLY32 4.2 34.5 1.0 C B:TYR49 4.2 27.4 1.0 HB3 B:ASN91 4.2 56.9 1.0 HA B:LEU33 4.3 43.1 1.0 HB3 B:TYR49 4.3 34.2 1.0 HG2 A:PRO151 4.3 47.2 1.0 CB B:ALA34 4.3 32.6 1.0 H B:ALA34 4.4 34.3 1.0 HA B:ALA34 4.4 40.5 1.0 H B:SER51 4.4 39.0 1.0 CA B:ALA34 4.5 33.6 1.0 HD3 A:PRO151 4.5 41.0 1.0 HA3 B:GLY32 4.5 40.1 1.0 CG B:ASP50 4.6 33.9 1.0 H B:ASN91 4.6 41.7 1.0 HB2 B:ALA34 4.8 39.3 1.0 O B:SER31 4.8 32.2 1.0 HB3 A:PRO151 4.9 43.9 1.0 CB B:ASP50 4.9 30.1 1.0 CD A:PRO151 4.9 34.1 1.0 HD2 B:TYR49 5.0 41.7 1.0 HB3 B:ALA34 5.0 39.3 1.0

R.Adams, C.Joyce, M.Kuravskiy, K.Harrison, Z.Ahdash, M.Balmforth, K.Chia, C.Marceddu, M.Coates, J.Snowden, E.Goursaud, K.Menochet, J.Van Den Elsen, R.J.Payne, A.D.G.Lawson, A.Scott-Tucker, A.Macpherson. Serum Albumin Binding Knob Domains Engineered Within A V H Framework III Bispecific Antibody Format and As Chimeric Peptides. Front Immunol V. 14 70357 2023.
ISSN: ESSN 1664-3224
PubMed: 37251411
DOI: 10.3389/FIMMU.2023.1170357