SMTL ID : 6k1q.1

Human endothelin receptor type-B in complex with inverse agonist IRL2500

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x D2U: (2~{S})-2-[[(2~{R})-2-[(3,5-dimethylphenyl)carbonyl-methyl-amino]-3-(4-phenylphenyl)propanoyl]amino]-3-(1~{H}-indol-3-yl)propanoic acid(Non-covalent)

D2U.1: 24 residues within 4Å: Chain A: D.85, H.88, N.96, K.99, W.105, C.112, V.115, P.116, Q.119, K.120, S.122, V.123, T.126, F.178, L.215, Y.219, W.384, L.387, H.388, R.391, A.423, S.424, N.426, S.427 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:K.99, A:W.105, A:V.115, A:P.116, A:Q.119, A:K.120, A:V.123, A:V.123, A:F.178, A:L.215, A:L.215, A:Y.219, A:W.384, A:W.384, A:W.384, A:L.387 Hydrogen bonds: A:N.96, A:Q.119 Water bridges: A:K.120, A:R.391 Salt bridges: A:R.391 pi-Stacking: A:H.88, A:W.384 pi-Cation interactions: A:K.99, A:K.99

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: L.239, I.243, Y.285, A.290, R.293, A.294, I.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.285, A:Y.285 PO4.3: 5 residues within 4Å: Chain A: C.69, M.70, R.440, N.443, A.444 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.443, A:A.444 Salt bridges: A:R.440 PO4.4: 3 residues within 4Å: Chain A: D.250, R.342, R.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.250, A:D.250, A:R.342 Salt bridges: A:R.345 PO4.5: 3 residues within 4Å: Chain A: Y.435, K.442, K.446 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.435, A:Y.435 Salt bridges: A:K.446

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

OLC.6: 7 residues within 4Å: Chain A: V.169, L.170, P.173, T.201, F.203, Y.207, W.214 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.169, A:P.173, A:F.203, A:W.214, A:W.214, A:W.214 Hydrogen bonds: A:T.201 OLC.7: 7 residues within 4Å: Chain A: T.209, A.210, W.213, W.214, S.217, L.222 Ligands: OLC.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.210, A:W.213, A:W.214, A:L.222 OLC.8: 6 residues within 4Å: Chain A: A.202, F.203, F.206, W.214, F.218 Ligands: OLC.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.203, A:F.206, A:F.206, A:W.214, A:F.218 OLC.9: 3 residues within 4Å: Chain A: S.80, L.83, W.164 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.83, A:W.164, A:W.164, A:W.164 OLC.10: 11 residues within 4Å: Chain A: K.371, C.375, V.379, A.429, I.432, A.433, L.436, V.437, K.439, K.442 Ligands: OLC.11 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.379, A:A.429, A:I.432, A:A.433, A:L.436, A:L.436, A:V.437 Hydrogen bonds: A:K.442, A:K.442 Salt bridges: A:K.371 OLC.11: 11 residues within 4Å: Chain A: L.224, T.227, A.228, Y.231, F.374, C.375, V.377, L.378, V.379, L.382 Ligands: OLC.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.231, A:F.374, A:L.382 OLC.12: 7 residues within 4Å: Chain A: I.34, T.37, F.38, I.41, N.421, M.422, L.425 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.38, A:I.41, A:N.421 OLC.13: 7 residues within 4Å: Chain A: L.87, K.113, L.114, F.117, A.121, V.168, A.175 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.113, A:F.117, A:A.121, A:V.168, A:V.168, A:A.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagiri, C. et al., Crystal structure of human endothelin ETBreceptor in complex with peptide inverse agonist IRL2500. Commun Biol (2019)

Release Date

2019-07-17

Peptides

Endothelin B receptor,Endolysin,Endothelin B 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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Endothelin B receptor,Endolysin,Endothelin B receptor

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