SMTL ID : 6q4r.1

High-resolution crystal structure of ERAP1 with bound phosphinic transition-state analogue inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: H.99, L.100, Q.101, A.152, N.154 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: H.68, A.69, N.70, E.210 Ligands: EDO.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.229

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: N.414, M.525 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.414, A:N.414 NAG.4: 2 residues within 4Å: Chain A: K.338, N.735 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.735

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.353, H.357, E.376, Y.438 Ligands: HJ5.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.353, A:H.357, A:E.376, A:E.376

1 x HJ5: [(1~{R})-1-[[(2~{S})-2-[[(2~{S})-1-azaniumyl-1-oxidanylidene-3-phenyl-propan-2-yl]carbamoyl]pent-4-ynyl]-oxidanyl-phosphoryl]-3-phenyl-propyl]azanium(Non-covalent)

HJ5.6: 24 residues within 4Å: Chain A: Q.181, E.183, P.184, Q.315, S.316, G.317, A.318, M.319, E.320, T.350, H.353, E.354, H.357, E.376, K.380, E.383, F.433, Y.438, S.844 Ligands: ZN.5, EDO.27, EDO.31, NA.41, NA.42 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.353, A:F.433 Hydrogen bonds: A:E.183, A:G.317, A:A.318, A:Y.438 Water bridges: A:K.380, A:K.380 pi-Stacking: A:F.433

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.7: 15 residues within 4Å: Chain A: F.405, D.406, E.409, K.526, N.616, S.623, Q.650, N.653, E.654, P.657, M.658, L.661, E.892, N.893, W.896 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:D.406, A:K.526, A:N.616, A:S.623, A:Q.650, A:P.657, A:E.892, A:E.892 Water bridges: A:G.402, A:F.405, A:E.409, A:E.409, A:K.526, A:N.616, A:S.623, A:Q.650, A:N.653

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

EDO.8: 11 residues within 4Å: Chain A: H.98, E.129, H.160, T.185, A.186, R.188, M.189, P.426, R.430, E.840 Ligands: EDO.12 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: S.340, A.341, S.342, R.700, M.701, S.704, D.741 Ligands: EDO.26 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: D.550, M.551, V.552 Ligands: P6G.39 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: F.555, V.563, L.564, I.565 Ligands: EDO.25, P6G.39 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain A: I.52, R.127, Q.128, E.129, R.188, N.425, P.426 Ligands: EDO.8, EDO.17 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain A: F.76, N.154, L.155, S.156, H.160, G.161, F.162, M.189, A.190 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: A.427, L.841, K.874, E.875, G.877, S.878, Q.879, L.880 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: N.370, D.371, S.420, T.421, P.422, L.501 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: F.544, S.549, H.553, L.566, P.567 Ligands: P6G.39 Ligand excluded by PLIP EDO.17: 12 residues within 4Å: Chain A: I.52, H.96, T.185, R.188, D.195, E.196, W.368, E.424, N.425, P.426, I.429 Ligands: EDO.12 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: T.643, E.644, I.645, S.698, E.699, L.702 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain A: H.417, T.421, P.422, V.423, Q.428, E.431, M.432, R.881 Ligands: EDO.36 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: R.515, P.567, E.568, E.569 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: W.691, R.721, Y.725 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain A: M.662, E.663, K.664, R.665, M.667, N.668, E.671, P.818, Y.821 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: L.66, H.68, W.77, G.78, T.79, H.150, R.208 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: K.548, E.568 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: I.565 Ligands: EDO.11, P6G.39 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain A: S.340, S.342, S.704, V.740, L.744, T.771, Q.775 Ligands: EDO.9 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: F.433, D.434, D.435, Y.438, S.844, H.848 Ligands: HJ5.6 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: R.829, K.830, W.832, N.833, F.869 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain A: A.198, E.367, K.471, N.472 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: R.665, M.667, M.897, D.898, F.901 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: Q.315, S.316, G.317, R.328 Ligands: HJ5.6 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain A: F.649, L.652, N.653, I.656, Q.705 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain A: H.68, A.69, N.70, T.75, F.76, W.77 Ligands: NAG-NAG-BMA.2 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain A: P.48, W.49, N.50, K.51 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain A: K.338, W.729, L.736, S.737, L.738, T.743, F.747, E.772 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: S.416, H.417, P.418, T.421, R.881 Ligands: EDO.19 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain A: N.497, T.498, L.501, Q.502 Ligand excluded by PLIP

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

MLT.38: 9 residues within 4Å: Chain A: I.656, Y.659, K.660, Q.705, L.708, L.709, V.712, H.713, R.782 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.659, A:Y.659 Water bridges: A:K.660, A:L.709, A:R.782, A:R.782 Salt bridges: A:K.660, A:R.782

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.39: 12 residues within 4Å: Chain A: F.544, M.551, V.552, H.553, R.554, F.555, L.564, I.565 Ligands: EDO.10, EDO.11, EDO.16, EDO.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.554, A:R.554

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

PG4.40: 15 residues within 4Å: Chain A: N.446, M.447, E.450, Y.451, P.541, L.542, T.543, R.554, F.555, L.556, N.576, V.577, N.580, G.581, Y.583 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.543, A:R.554, A:Y.583, A:Y.583 Water bridges: A:Y.451

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

NA.41: 5 residues within 4Å: Chain A: Q.315, S.843, S.844, S.845 Ligands: HJ5.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.315, A:S.844, A:S.845 NA.42: 5 residues within 4Å: Chain A: Q.181, F.314, Q.315, S.316 Ligands: HJ5.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.315, A:S.316, A:S.316 NA.43: 4 residues within 4Å: Chain A: E.431, L.880, R.881, C.882 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.431, A:R.881, A:C.882 Water bridges: A:G.842

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giastas, P. et al., High-Resolution Crystal Structure of Endoplasmic Reticulum Aminopeptidase 1 with Bound Phosphinic Transition-State Analogue Inhibitor. Acs Med.Chem.Lett. (2019)

Release Date

2019-04-10

Peptides

Endoplasmic reticulum aminopeptidase 1,Endoplasmic reticulum aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoplasmic reticulum aminopeptidase 1,Endoplasmic reticulum aminopeptidase 1