Chlorine in PDB 9hgd: Crystal Structure of Human Gabarap in Complex with Cyclic Peptide GAB_D23

The structure of Crystal Structure of Human Gabarap in Complex with Cyclic Peptide GAB_D23, PDB code: 9hgd was solved by A.Ueffing, J.A.Wilms, D.Willbold, O.H.Weiergraeber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.42 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.63, 43.79, 67.52, 90, 128.38, 90
R / Rfree (%)	18.8 / 22.2

The binding sites of Chlorine atom in the Crystal Structure of Human Gabarap in Complex with Cyclic Peptide GAB_D23 (pdb code 9hgd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Human Gabarap in Complex with Cyclic Peptide GAB_D23, PDB code: 9hgd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Human Gabarap in Complex with Cyclic Peptide GAB_D23


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Gabarap in Complex with Cyclic Peptide GAB_D23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:27.7 occ:0.84 OE1 A:GLU8 2.4 30.5 0.2 NZ A:LYS47 3.0 33.1 1.0 O A:HOH310 3.2 27.5 1.0 CD A:GLU8 3.6 26.8 0.2 CE1 A:HIS9 3.7 32.5 1.0 CE A:LYS47 3.7 33.1 1.0 O A:HOH312 3.7 33.1 1.0 CD2 A:TYR5 3.7 33.3 1.0 CG A:GLU8 3.8 26.1 0.8 CD A:LYS47 3.8 27.8 1.0 CA A:TYR5 3.9 25.1 1.0 CB A:GLU8 4.1 25.3 0.8 CB A:GLU8 4.3 27.1 0.2 CB A:TYR5 4.3 28.6 1.0 CG A:GLU8 4.3 27.0 0.2 N A:TYR5 4.4 28.6 1.0 ND1 A:HIS9 4.4 28.4 1.0 CG A:TYR5 4.4 27.6 1.0 CE2 A:TYR5 4.6 30.2 1.0 OE2 A:GLU8 4.6 28.4 0.2 CD A:GLU8 4.7 25.2 0.8 O A:HOH338 4.7 36.0 1.0 NE2 A:HIS9 4.7 36.6 1.0 CG1 A:VAL4 4.8 32.0 1.0 C A:VAL4 4.8 30.8 1.0 O A:VAL4 4.9 30.0 1.0 OE2 A:GLU8 5.0 27.6 0.8

Chlorine binding site 2 out of 2 in the Crystal Structure of Human Gabarap in Complex with Cyclic Peptide GAB_D23


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Gabarap in Complex with Cyclic Peptide GAB_D23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:26.7 occ:1.00 N A:ASP27 3.3 23.5 1.0 NH1 A:ARG28 3.4 29.1 1.0 C A:TYR25 3.4 24.7 1.0 CA A:TYR25 3.5 24.9 1.0 N A:PRO26 3.7 23.5 1.0 CB A:ASP27 3.7 27.8 1.0 N A:ARG28 3.8 21.5 1.0 CA A:ASP27 3.8 24.4 1.0 CB A:TYR25 3.8 26.9 1.0 CD A:ARG28 3.8 24.6 1.0 O A:TYR25 3.8 24.2 1.0 CG A:ARG28 3.9 21.9 1.0 C A:ASP27 3.9 27.5 1.0 CD A:PRO26 4.0 23.5 1.0 CB A:ARG28 4.2 22.7 1.0 CD1 A:TYR25 4.3 28.2 1.0 C A:PRO26 4.3 26.6 1.0 CZ A:ARG28 4.4 32.3 1.0 NE A:ARG28 4.6 27.6 1.0 CA A:PRO26 4.6 25.5 1.0 CG A:TYR25 4.6 27.3 1.0 CA A:ARG28 4.6 24.9 1.0 O A:ASP27 4.7 28.4 1.0 CG A:PRO26 4.8 24.5 1.0 N A:TYR25 4.9 23.1 1.0 CG A:ASP27 4.9 30.5 1.0 OD2 A:ASP27 4.9 35.5 1.0

S.A.Rettie, D.Juergens, V.Adebomi, Y.F.Bueso, Q.Zhao, A.N.Leveille, A.Liu, A.K.Bera, J.A.Wilms, A.Uffing, A.Kang, E.Brackenbrough, M.Lamb, S.R.Gerben, A.Murray, P.M.Levine, M.Schneider, V.Vasireddy, S.Ovchinnikov, O.H.Weiergraber, D.Willbold, J.A.Kritzer, J.D.Mougous, D.Baker, F.Dimaio, G.Bhardwaj. Accurate De Novo Design of High-Affinity Protein-Binding Macrocycles Using Deep Learning. Nat.Chem.Biol. 2025.
ISSN: ESSN 1552-4469
PubMed: 40542165
DOI: 10.1038/S41589-025-01929-W