SMTL ID : 5ee7.1

Crystal structure of the human glucagon receptor (GCGR) in complex with the antagonist MK-0893

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x 5MV: 3-[[4-[(1~{S})-1-[3-[3,5-bis(chloranyl)phenyl]-5-(6-methoxynaphthalen-2-yl)pyrazol-1-yl]ethyl]phenyl]carbonylamino]propanoic acid(Non-covalent)

5MV.1: 16 residues within 4Å: Chain A: L.351, F.367, R.368, A.370, K.371, S.372, L.374, T.375, L.421, L.425, N.426, K.427 Ligands: OLA.11, OLA.12, OLA.13, OLA.14 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.368, A:K.371, A:K.371, A:L.374, A:T.375, A:L.421 Hydrogen bonds: A:K.371, A:S.372, A:N.426, A:K.427 Salt bridges: A:R.368

14 x OLA: OLEIC ACID(Non-covalent)(Non-functional Binders)

OLA.2: 2 residues within 4Å: Chain A: L.290, W.294 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.294 OLA.3: 2 residues within 4Å: Chain A: A.402, K.403 No protein-ligand interaction detected (PLIP) OLA.4: 7 residues within 4Å: Chain A: H.383, D.407, L.410, F.413, Q.414, L.416 Ligands: OLA.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.410, A:L.416 Hydrogen bonds: A:D.407 Salt bridges: A:H.383 OLA.5: 5 residues within 4Å: Chain A: T.11, V.12, S.15, L.57 Ligands: OLA.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.12 Hydrogen bonds: A:S.15, A:S.15 OLA.6: 4 residues within 4Å: Chain A: Q.7, V.8, T.11 Ligands: OLA.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.11 Water bridges: A:Q.7 OLA.7: 8 residues within 4Å: Chain A: L.18, L.22, L.25, L.47, V.50, S.54, L.57, F.58 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.18, A:L.25, A:L.25, A:L.47, A:V.50 OLA.8: 6 residues within 4Å: Chain A: C.36, T.37, A.40, N.44, F.286, W.294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.40, A:F.286, A:W.294, A:W.294 OLA.9: 5 residues within 4Å: Chain A: H.115, L.335, I.339, F.342, R.346 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.335, A:I.339, A:I.339, A:F.342 Salt bridges: A:H.115, A:R.346 OLA.10: 8 residues within 4Å: Chain A: D.83, V.86, A.87, R.90, V.91, V.94, V.302, W.317 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.86, A:R.90, A:V.91, A:V.94, A:V.302, A:W.317 OLA.11: 2 residues within 4Å: Ligands: 5MV.1, OLA.12 No protein-ligand interaction detected (PLIP) OLA.12: 4 residues within 4Å: Chain A: F.367 Ligands: 5MV.1, OLA.11, OLA.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.367 OLA.13: 5 residues within 4Å: Chain A: F.344, V.348, L.374 Ligands: 5MV.1, OLA.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.344, A:V.348 OLA.14: 2 residues within 4Å: Ligands: 5MV.1, OLA.4 No protein-ligand interaction detected (PLIP) OLA.15: 2 residues within 4Å: Chain A: L.62, A.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.82

1 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.16: 17 residues within 4Å: Chain A: F.6, Y.10, Y.14, F.49, K.52, V.56, I.59, R.64, I.100, N.103, Y.104, T.318, M.323, F.325, H.383, F.387, Q.414 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.100, A:Y.104 Hydrogen bonds: A:Y.14, A:R.64, A:R.64, A:Y.104, A:Q.414 Water bridges: A:K.52, A:S.411

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.17: 7 residues within 4Å: Chain A: I.337, N.340, F.341, I.377, P.378, G.381, V.382 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jazayeri, A. et al., Extra-helical binding site of a glucagon receptor antagonist. Nature (2016)

Release Date

2016-04-20

Peptides

Glucagon receptor,Endolysin,Glucagon 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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Glucagon receptor,Endolysin,Glucagon receptor