SMTL ID : 7br3.1

Crystal structure of the protein 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

monomer

Ligands

1 x 1QW: (2R)-2,3-dihydroxypropyl dodecanoate(Non-covalent)

1QW.1: 4 residues within 4Å: Chain A: L.236, I.243, T.467, V.468 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.243, A:T.467, A:V.468

2 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 1 residues within 4Å: Chain A: S.42 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.46 OLC.3: 3 residues within 4Å: Chain A: W.479, F.482, D.483 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.482 Hydrogen bonds: A:D.483

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 2 residues within 4Å: Chain A: S.148, L.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.148 PEG.5: 2 residues within 4Å: Chain A: L.145, I.234 No protein-ligand interaction detected (PLIP) PEG.6: 4 residues within 4Å: Chain A: F.138, V.141, V.142, L.174 No protein-ligand interaction detected (PLIP) PEG.7: 3 residues within 4Å: Chain A: E.259, L.262, G.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.259, A:G.264 PEG.8: 3 residues within 4Å: Chain A: T.59, F.60, S.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.59, A:S.63 PEG.9: 3 residues within 4Å: Chain A: W.257, R.352, E.380 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.352

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.10: 2 residues within 4Å: Chain A: E.316, L.424 No protein-ligand interaction detected (PLIP)

1 x F5O: 4-[[(1R)-2-[5-(2-fluoranyl-3-methoxy-phenyl)-3-[[2-fluoranyl-6-(trifluoromethyl)phenyl]methyl]-4-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]-1-phenyl-ethyl]amino]butanoic acid(Non-covalent)

F5O.11: 19 residues within 4Å: Chain A: I.29, P.30, L.31, Q.33, G.34, D.106, N.110, I.111, K.129, T.223, F.224, L.227, Y.473, L.476, G.477, M.486, L.487, N.495, F.498 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.30, A:L.31, A:D.106, A:L.227, A:L.476, A:L.487 Hydrogen bonds: A:Q.33, A:D.106, A:K.129, A:Y.473 pi-Stacking: A:Y.480

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, W. et al., Structure of the human gonadotropin-releasing hormone receptor GnRH1R reveals an unusual ligand binding mode. Nat Commun (2020)

Release Date

2020-10-07

Peptides

Gonadotropin-releasing hormone receptor,GlgA glycogen synthase,Gonadotropin-releasing hormone receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Gonadotropin-releasing hormone receptor,GlgA glycogen synthase,Gonadotropin-releasing hormone receptor