SMTL ID : 6tod.1 (1 other biounit)

Crystal structure of the Orexin-1 receptor in complex with EMPA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

1 x 7MA: N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide(Non-covalent)

7MA.1: 20 residues within 4Å: Chain A: S.79, W.88, I.98, P.99, Q.102, T.103, V.106, Q.155, M.159, C.178, E.180, H.192, F.195, Y.255, I.258, S.259, N.262, H.288, V.291, Y.292 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.88, A:P.99, A:Q.102, A:F.195, A:F.195, A:I.258 Hydrogen bonds: A:S.79, A:Q.155

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: K.239, S.306, G.307, K.308 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.307, A:K.308 Water bridges: A:A.236, A:T.240 Salt bridges: A:K.239

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: C.178, D.179, K.265, F.271, R.272, V.280, F.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.265 Water bridges: A:E.86, A:R.266, A:R.266, A:R.272 PG4.4: 7 residues within 4Å: Chain A: L.204, A.208, Y.211, F.212, M.245, V.248 Ligands: SOG.26 No protein-ligand interaction detected (PLIP) PG4.5: 4 residues within 4Å: Chain A: L.253, L.290, A.293, A.297 No protein-ligand interaction detected (PLIP)

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 7 residues within 4Å: Chain A: T.55, V.56, T.57, R.120, Q.233, R.237, T.240 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:V.56, A:T.57, A:T.57, A:R.120, A:Q.233 Water bridges: A:T.55, A:T.55, A:R.120 Salt bridges: A:R.120, A:R.120, A:R.237

22 x SOG: octyl 1-thio-beta-D-glucopyranoside(Non-covalent)(Non-functional Binders)

SOG.7: 5 residues within 4Å: Chain A: F.90, L.94, R.173 Ligands: SOG.23, SOG.24 Ligand excluded by PLIP SOG.8: 8 residues within 4Å: Chain A: A.157, V.158, E.160, R.181, W.182, A.183, D.184, A.187 Ligand excluded by PLIP SOG.9: 7 residues within 4Å: Chain A: S.193, F.196, I.197, V.263, F.268 Ligands: SOG.10, SOG.17 Ligand excluded by PLIP SOG.10: 4 residues within 4Å: Chain A: F.268 Ligands: SOG.9, SOG.11, SOG.17 Ligand excluded by PLIP SOG.11: 6 residues within 4Å: Chain A: D.185, L.186, K.189, S.193, V.267 Ligands: SOG.10 Ligand excluded by PLIP SOG.12: 5 residues within 4Å: Chain A: W.121, H.126, L.129, Q.213 Ligands: PGW.29 Ligand excluded by PLIP SOG.13: 5 residues within 4Å: Chain A: K.96, Y.100, V.153, A.156, A.157 Ligand excluded by PLIP SOG.14: 7 residues within 4Å: Chain A: F.115, R.136, G.139, S.140, G.143, I.144, V.147 Ligand excluded by PLIP SOG.15: 6 residues within 4Å: Chain A: V.30, F.33, L.76, P.77, L.80 Ligands: SOG.23 Ligand excluded by PLIP SOG.16: 6 residues within 4Å: Chain A: L.66, V.69, L.70, L.142, W.145, L.149 Ligand excluded by PLIP SOG.17: 9 residues within 4Å: Chain A: F.196, V.260, V.263, L.264, F.268, M.270 Ligands: SOG.9, SOG.10, SOG.18 Ligand excluded by PLIP SOG.18: 4 residues within 4Å: Chain A: L.256, M.270 Ligands: SOG.17, SOG.21 Ligand excluded by PLIP SOG.19: 2 residues within 4Å: Chain A: A.208, F.212 Ligand excluded by PLIP SOG.20: 4 residues within 4Å: Chain A: F.215, W.219, M.245, V.246 Ligand excluded by PLIP SOG.21: 5 residues within 4Å: Chain A: V.260, L.264, M.270 Ligands: SOG.18, SOG.22 Ligand excluded by PLIP SOG.22: 6 residues within 4Å: Chain A: F.271, D.276, A.279, V.280, A.283 Ligands: SOG.21 Ligand excluded by PLIP SOG.23: 4 residues within 4Å: Chain A: L.81 Ligands: SOG.7, SOG.15, SOG.25 Ligand excluded by PLIP SOG.24: 3 residues within 4Å: Chain A: L.81, L.89 Ligands: SOG.7 Ligand excluded by PLIP SOG.25: 4 residues within 4Å: Chain A: A.73, I.74, F.90 Ligands: SOG.23 Ligand excluded by PLIP SOG.26: 1 residues within 4Å: Ligands: PG4.4 Ligand excluded by PLIP SOG.27: 4 residues within 4Å: Chain A: G.91, H.92, A.93, R.173 Ligand excluded by PLIP SOG.28: 5 residues within 4Å: Chain A: W.48, R.54, Y.59, V.62, L.138 Ligand excluded by PLIP

1 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.29: 13 residues within 4Å: Chain A: S.114, A.117, L.118, W.121, V.198, G.205, L.206, M.209, A.210, F.212, Q.213, R.216 Ligands: SOG.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.117, A:L.118, A:W.121, A:L.206, A:L.206, A:L.206, A:M.209, A:A.210 Hydrogen bonds: A:Q.213, A:R.216

1 x NA: SODIUM ION(Non-functional Binders)

NA.30: 3 residues within 4Å: Chain A: D.68, Y.255, N.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.255, A:Y.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rappas, M. et al., Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-ray Crystallography and Computational Analysis. J.Med.Chem. (2020)

Release Date

2020-01-01

Peptides

Orexin receptor type 1: 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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Orexin receptor type 1

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