Iodine in PDB 6b73: Crystal Structure of A Nanobody-Stabilized Active State of the Kappa- Opioid Receptor

The structure of Crystal Structure of A Nanobody-Stabilized Active State of the Kappa- Opioid Receptor, PDB code: 6b73 was solved by T.Che, S.Majumdar, S.A.Zaidi, C.Kormos, J.D.Mccorvy, S.Wang, P.D.Mosier, R.Uprety, E.Vardy, B.E.Krumm, G.W.Han, M.Y.Lee, E.Pardon, J.Steyaert, X.P.Huang, R.T.Strachan, A.R.Tribo, G.W.Pasternak, I.F.Carroll, R.C.Stevens, V.Cherezov, V.Katritch, D.Wacker, B.L.Roth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.94 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.310, 150.750, 100.280, 90.00, 105.66, 90.00
R / Rfree (%)	25.4 / 27.5

The binding sites of Iodine atom in the Crystal Structure of A Nanobody-Stabilized Active State of the Kappa- Opioid Receptor (pdb code 6b73). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of A Nanobody-Stabilized Active State of the Kappa- Opioid Receptor, PDB code: 6b73:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of A Nanobody-Stabilized Active State of the Kappa- Opioid Receptor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of A Nanobody-Stabilized Active State of the Kappa- Opioid Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:I2001 b:98.8 occ:1.00 I1 A:CVV2001 0.0 98.8 1.0 C12 A:CVV2001 2.1 95.9 1.0 C11 A:CVV2001 3.0 93.8 1.0 C13 A:CVV2001 3.1 93.8 1.0 CG1 A:VAL134 3.3 70.6 1.0 OD2 A:ASP138 3.5 94.0 1.0 NE2 A:GLN115 3.9 52.7 1.0 CG A:ASP138 3.9 86.2 1.0 CD A:GLN115 3.9 68.8 1.0 CB A:THR111 3.9 65.5 1.0 O A:THR111 4.0 63.0 1.0 CG A:GLN115 4.0 61.8 1.0 CB A:ASP138 4.1 72.6 1.0 OH A:TYR320 4.2 70.5 1.0 OG1 A:THR111 4.3 60.0 1.0 O A:VAL134 4.3 72.5 1.0 OE1 A:GLN115 4.3 64.4 1.0 CB A:PHE114 4.4 64.3 1.0 C10 A:CVV2001 4.4 90.3 1.0 C14 A:CVV2001 4.4 92.1 1.0 OD1 A:ASP138 4.5 86.3 1.0 C A:THR111 4.6 64.1 1.0 CG2 A:THR111 4.7 63.4 1.0 CA A:THR111 4.7 61.4 1.0 CB A:VAL134 4.7 72.2 1.0 C A:VAL134 4.7 73.0 1.0 N A:GLN115 4.8 62.8 1.0 C15 A:CVV2001 4.9 91.3 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of A Nanobody-Stabilized Active State of the Kappa- Opioid Receptor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of A Nanobody-Stabilized Active State of the Kappa- Opioid Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:I2001 b:98.0 occ:1.00 I1 B:CVV2001 0.0 98.0 1.0 C12 B:CVV2001 2.1 95.2 1.0 C11 B:CVV2001 3.1 93.1 1.0 C13 B:CVV2001 3.1 93.2 1.0 CG1 B:VAL134 3.3 74.5 1.0 CB B:THR111 3.8 66.7 1.0 OD2 B:ASP138 3.8 87.5 1.0 CG B:ASP138 3.9 84.2 1.0 O B:THR111 3.9 71.6 1.0 CB B:ASP138 4.0 74.0 1.0 CG B:GLN115 4.1 83.2 1.0 CD B:GLN115 4.1 96.1 1.0 OH B:TYR320 4.1 66.1 1.0 NE2 B:GLN115 4.1 90.1 1.0 OG1 B:THR111 4.2 59.0 1.0 O B:VAL134 4.3 74.6 1.0 OD1 B:ASP138 4.4 84.7 1.0 C14 B:CVV2001 4.4 91.0 1.0 C10 B:CVV2001 4.4 90.1 1.0 CB B:PHE114 4.5 72.6 1.0 OE1 B:GLN115 4.5 87.2 1.0 C B:THR111 4.5 71.9 1.0 CG2 B:THR111 4.6 64.6 1.0 CA B:THR111 4.6 66.0 1.0 C B:VAL134 4.7 76.3 1.0 CB B:VAL134 4.7 75.7 1.0 N B:GLN115 4.9 71.3 1.0 C15 B:CVV2001 4.9 90.3 1.0

T.Che, S.Majumdar, S.A.Zaidi, P.Ondachi, J.D.Mccorvy, S.Wang, P.D.Mosier, R.Uprety, E.Vardy, B.E.Krumm, G.W.Han, M.Y.Lee, E.Pardon, J.Steyaert, X.P.Huang, R.T.Strachan, A.R.Tribo, G.W.Pasternak, F.I.Carroll, R.C.Stevens, V.Cherezov, V.Katritch, D.Wacker, B.L.Roth. Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor. Cell V. 172 55 2018.
ISSN: ISSN 1097-4172
PubMed: 29307491
DOI: 10.1016/J.CELL.2017.12.011