SMTL ID : 6t6r.1

Human endoplasmic reticulum aminopeptidase 1 (ERAP1) in complex with (4aR,5S,6R,8S,8aR)-5-(2-(Furan-3-yl)ethyl)-8-hydroxy-5,6,8a-trimethyl-3,4,4a,5,6,7,8,8a-octahydronaphthalene-1-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.353, H.357, E.376, Y.438 Ligands: MLT.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.353, A:H.357, A:E.376, A:E.376

2 x MLT: D-MALATE(Non-covalent)

MLT.2: 11 residues within 4Å: Chain A: G.317, A.318, E.320, T.350, H.353, E.354, H.357, E.376, Y.438 Ligands: ZN.1, EDO.10 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.317, A:A.318, A:E.354, A:Y.438 Water bridges: A:K.380 Salt bridges: A:H.353, A:H.353, A:H.357, A:K.380 MLT.3: 7 residues within 4Å: Chain A: T.79, K.81, R.104, R.108, E.117, V.148, H.150 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.104 Water bridges: A:R.108 Salt bridges: A:K.81, A:R.108, A:R.108, A:H.150, A:H.150

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: P.657, L.661, W.896 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: S.340, A.341, S.342, R.700, M.701, S.704, D.741 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: R.665, M.667, M.897, D.898, F.901 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: A.751, Q.752, S.753, T.754, T.783, N.785, K.788 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: R.430, F.433, S.843, S.844 Ligands: EDO.11 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: H.98, E.129, T.185, A.186, M.189, P.426, R.430, E.840 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: Q.181, S.316, A.318, M.319 Ligands: MLT.2, EDO.11 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: S.316, Y.438 Ligands: EDO.8, EDO.10, EDO.13 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: S.416, H.417, P.418, T.421, R.881 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: Q.315, S.316, S.844, S.845, H.848 Ligands: EDO.11, EDO.15 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: R.829, K.830, N.833, F.869 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: Q.315, S.316, G.317, R.328 Ligands: EDO.13 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: T.421, V.423, Q.428, E.431, M.432, R.881 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: T.643, E.644, I.645, S.696, S.698, E.699, L.702 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: Y.296, R.449, A.454, D.455, K.458 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: A.69, L.71, R.209, E.210, H.213, I.251 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Chain A: R.829 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: F.159, K.164, D.313, K.838 Ligand excluded by PLIP

1 x MNZ: (4~{a}~{R},5~{S},6~{R},8~{S},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-8-oxidanyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid(Non-covalent)

MNZ.22: 12 residues within 4Å: Chain A: F.649, L.652, N.653, I.656, Y.659, K.660, Q.705, L.708, L.709, H.713, F.778, R.782 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.652, A:I.656, A:Q.705, A:L.708, A:L.709, A:F.778 Water bridges: A:R.782, A:R.782 Salt bridges: A:K.660, A:R.782 pi-Stacking: A:F.649

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liddle, J. et al., Targeting the Regulatory Site of ER Aminopeptidase 1 Leads to the Discovery of a Natural Product Modulator of Antigen Presentation. J.Med.Chem. (2020)

Release Date

2020-03-18

Peptides

Endoplasmic reticulum aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoplasmic reticulum aminopeptidase 1