SMTL ID : 6rqx.1

High-resolution crystal structure of ERAP1 in complex with 10mer phosphinic peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

1 x KF2- LYS- HIS- HIS- ALA- PHE- SER- PHE- LYS: PSE-LYS-HIS-HIS-ALA-PHE-SER-PHE-LYS(Non-covalent)

KF2-LYS-HIS-HIS-ALA-PHE-SER-PHE-LYS.1: 48 residues within 4Å: Chain A: Q.181, E.183, P.184, Q.315, S.316, G.317, A.318, M.319, E.320, R.328, S.330, A.331, S.340, A.341, S.342, S.343, G.346, I.347, T.350, H.353, E.354, H.357, E.376, K.380, F.433, D.434, D.435, Y.438, D.439, R.725, M.726, S.729, D.766, L.769, S.795, T.796, S.799, Q.800, E.802, E.831, Q.834, L.838, S.869, H.873 Ligands: ZN.6, SCN.8, SCN.14, NA.43 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:T.350, A:H.353, A:Y.438, A:Q.834, A:L.838 Hydrogen bonds: A:E.183, A:G.317, A:A.341, A:K.380, A:Y.438, A:Y.438, A:Y.438, A:S.729, A:S.729, A:D.766, A:S.795, A:S.799, A:Q.800, A:H.873 Water bridges: A:R.328, A:S.342, A:S.342 pi-Stacking: A:F.433

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.2: 1 residues within 4Å: Chain A: N.760 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.335

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.3: 8 residues within 4Å: Chain A: H.68, A.69, N.70, E.210, E.229, L.231 Ligands: SCN.7, EDO.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.229

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.4: 6 residues within 4Å: Chain A: H.99, L.100, Q.101, A.152, G.153, N.154 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.414, M.550 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.414

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.353, H.357, E.376, Y.438 Ligands: KF2-LYS-HIS-HIS-ALA-PHE-SER-PHE-LYS.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.353, A:H.357, A:E.376, A:E.376

11 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.7: 8 residues within 4Å: Chain A: A.69, N.70, L.71, R.209, E.210, H.213, I.251 Ligands: NAG-NAG-BMA-MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.71 SCN.8: 6 residues within 4Å: Chain A: Q.315, S.316, S.869, S.870 Ligands: KF2-LYS-HIS-HIS-ALA-PHE-SER-PHE-LYS.1, NA.40 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.869 SCN.9: 6 residues within 4Å: Chain A: A.427, E.900, G.902, S.903, Q.904, L.905 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.902, A:Q.904 SCN.10: 4 residues within 4Å: Chain A: I.299, P.300, L.363, Y.470 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.470 Water bridges: A:S.469 SCN.11: 5 residues within 4Å: Chain A: E.547, H.548, Y.549, M.550, A.556 No protein-ligand interaction detected (PLIP) SCN.12: 4 residues within 4Å: Chain A: Y.296, R.449, F.457, I.461 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.296, A:R.449 SCN.13: 5 residues within 4Å: Chain A: L.66, W.77, G.78, T.79, R.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.208 SCN.14: 6 residues within 4Å: Chain A: S.330, A.331 Ligands: KF2-LYS-HIS-HIS-ALA-PHE-SER-PHE-LYS.1, KF2-LYS-HIS-HIS-ALA-PHE-SER-PHE-LYS.1, KF2-LYS-HIS-HIS-ALA-PHE-SER-PHE-LYS.1, KF2-LYS-HIS-HIS-ALA-PHE-SER-PHE-LYS.1 No protein-ligand interaction detected (PLIP) SCN.15: 2 residues within 4Å: Chain A: R.885, K.892 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.892 SCN.16: 3 residues within 4Å: Chain A: R.53, W.368 Ligands: EDO.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.53, A:R.53 Water bridges: A:E.367 SCN.17: 3 residues within 4Å: Chain A: H.578, R.579, L.589 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.579

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

EDO.18: 9 residues within 4Å: Chain A: K.599, F.600, N.601, V.610, Y.612, W.617, S.638, L.639, N.642 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: H.417, T.421, P.422, V.423, Q.428, E.431, M.432, R.906 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: T.668, E.669, I.670, S.721, S.723, E.724, L.727 Ligand excluded by PLIP EDO.21: 10 residues within 4Å: Chain A: H.98, E.129, H.160, T.185, A.186, R.188, M.189, P.426, R.430, E.865 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: W.716, R.746, Y.750 Ligands: EDO.36 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: Y.451, P.566, L.567, R.579, F.580, L.581 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: N.370, D.371, S.420, K.474, N.475 Ligands: SCN.16 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: R.690, M.692, M.922, D.923, F.926 Ligands: PGE.44 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain A: V.537, W.597, I.598, Y.612, D.615, G.616, S.619, L.620 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: L.345, M.349, F.384, Y.399, K.403 Ligands: EDO.28 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain A: L.345, Y.399, F.674, M.726 Ligands: EDO.27, EDO.29 Ligand excluded by PLIP EDO.29: 9 residues within 4Å: Chain A: F.401, G.402, F.405, M.671, F.674, Q.675, N.678 Ligands: EDO.28, EDO.39 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain A: H.68, A.69, N.70, T.75, F.76, W.77 Ligands: NAG-NAG-BMA-MAN.3 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain A: F.334, D.335, A.336, E.337, K.338, S.339, D.718, R.725, V.765 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain A: F.292, Y.296, F.384, V.385, S.388, V.389, R.449 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain A: I.681, Y.684, K.685, H.738, R.807, R.841 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain A: R.854, K.855, W.857, N.858, F.894, L.898 Ligands: EDO.37 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain A: Q.904, L.905, R.906, Q.909 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: Q.714, T.715, W.716, T.717, R.746 Ligands: EDO.22 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain A: W.857, N.858, S.897, L.898, N.901 Ligands: EDO.34 Ligand excluded by PLIP EDO.38: 9 residues within 4Å: Chain A: L.662, F.702, R.705, W.932, L.933, S.935, E.936, K.937, L.938 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain A: F.674, L.677, N.678, Q.730 Ligands: EDO.29 Ligand excluded by PLIP

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

NA.40: 5 residues within 4Å: Chain A: Q.315, R.328, P.833, S.870 Ligands: SCN.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.328, A:S.870 NA.41: 5 residues within 4Å: Chain A: P.566, T.568, N.601, G.606, Y.608 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.566, A:T.568, A:Y.608 NA.42: 4 residues within 4Å: Chain A: V.602, G.603, S.632, D.635 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.632, A:D.635 Water bridges: A:S.632 NA.43: 4 residues within 4Å: Chain A: F.433, D.434, S.869 Ligands: KF2-LYS-HIS-HIS-ALA-PHE-SER-PHE-LYS.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.433

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.44: 8 residues within 4Å: Chain A: K.689, R.690, D.691, M.692, Y.846, T.884, R.887 Ligands: EDO.25 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.690, A:D.691, A:R.887, A:R.887 Water bridges: A:Y.846 PGE.45: 7 residues within 4Å: Chain A: P.847, W.850, Q.851, R.854, K.855, R.887, F.894 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.847, A:R.854, A:R.854 Water bridges: A:R.887 PGE.46: 7 residues within 4Å: Chain A: E.409, E.679, P.682, M.683, L.686, N.918, W.921 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.648, A:N.918

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giastas, P. et al., Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-12-18

Peptides

Endoplasmic reticulum aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoplasmic reticulum aminopeptidase 1