SMTL ID : 7z28.1

High-resolution crystal structure of ERAP1 with bound bestatin analogue inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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: 7 residues within 4Å: Chain A: H.24, A.25, N.26, E.166, E.185, G.186, L.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.185

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

NAG.2: 5 residues within 4Å: Chain A: H.55, Q.57, A.108, G.109, N.110 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.109, A:N.110

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.309, H.313, E.332 Ligands: I88.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.309, A:H.313, A:E.332

1 x I88: methyl (2~{S})-2-[[(2~{S})-2-[[(2~{S},3~{R})-3-azanyl-2,7-bis(oxidanyl)heptanoyl]amino]-4-methyl-pentanoyl]amino]-3-(4-hydroxyphenyl)propanoate(Non-covalent)

I88.4: 24 residues within 4Å: Chain A: Q.137, E.139, Q.271, S.272, G.273, A.274, M.275, E.276, R.284, T.306, H.309, E.310, H.313, E.332, K.336, E.339, F.389, Y.394, P.756, S.792, S.793, H.796 Ligands: ZN.3, EDO.20 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.306, A:H.309, A:F.389 Hydrogen bonds: A:G.273, A:A.274, A:A.274, A:E.276 pi-Stacking: A:H.796

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

EDO.5: 10 residues within 4Å: Chain A: H.54, E.85, H.116, T.141, A.142, R.144, M.145, P.382, R.386, E.788 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: H.373, T.377, P.378, V.379, Q.384, E.387, M.388, R.829 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: K.479, S.571, P.605, M.606, L.609, E.840, N.841, W.844 Ligands: PGE.24 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: S.296, A.297, S.298, R.648, M.649, S.652, D.689 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: A.699, Q.700, S.701, T.702, W.705, T.731, N.733, K.736 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: T.591, E.592, I.593, S.644, S.646, E.647, L.650 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: W.705, D.706, Y.709, K.736, W.739 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: R.613, M.615, M.845, D.846, F.849 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: F.503, D.510, V.511, L.512 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: V.465, W.520, I.521, Y.535, D.538, G.539, S.542, L.543 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: V.814, K.815, F.818, S.819, S.826, V.831, I.835 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: E.113, K.746, G.747, T.752, K.786 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: D.291, A.292, E.293, S.295, D.641, R.648, V.688 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: N.450, T.451, L.454, Q.455 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: R.777, K.778, W.780, N.781, F.817, L.821 Ligand excluded by PLIP EDO.20: 10 residues within 4Å: Chain A: F.115, H.116, Q.137, F.138, E.139, P.140, A.142, Q.271, E.788 Ligands: I88.4 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: K.588, H.589, E.590, T.591, D.632, L.633, K.636 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: F.597, L.600, N.601, Q.653 Ligand excluded by PLIP

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

MLT.23: 6 residues within 4Å: Chain A: I.604, Y.607, K.608, L.656, L.657, V.660 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.607, A:Y.607 Water bridges: A:K.608, A:K.608 Salt bridges: A:K.608

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

PGE.24: 13 residues within 4Å: Chain A: F.361, D.362, E.365, Y.477, K.479, N.564, F.567, Q.568, S.571, Q.598, N.601, E.602 Ligands: EDO.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.477, A:Y.477, A:K.479, A:Q.568, A:S.571, A:Q.598, A:N.601 Water bridges: A:N.564, A:N.564

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vourloumis, D. et al., Discovery of Selective Nanomolar Inhibitors for Insulin-Regulated Aminopeptidase Based on alpha-Hydroxy-beta-amino Acid Derivatives of Bestatin. J.Med.Chem. (2022)

Release Date

2022-07-27

Peptides

Endoplasmic reticulum aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoplasmic reticulum aminopeptidase 1