SMTL ID : 7p7p.1 (1 other biounit)

Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide((1R)-1-Amino-3-phenylpropyl){(2S)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)amino]-2-{[3-(2-hydroxyphenyl)-isoxazol-5-yl]methyl}-3-oxopropyl}phosphinic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

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.1: 6 residues within 4Å: Chain A: H.83, P.84, N.85, T.87, E.227, L.248 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-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.2: 8 residues within 4Å: Chain A: H.77, N.219, T.255, T.256, V.257, K.258, Y.487 Ligands: PEG.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.487

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.3: 2 residues within 4Å: Chain A: N.405, K.466 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.4: 2 residues within 4Å: Chain A: N.650, L.653 No protein-ligand interaction detected (PLIP)

1 x 62S: [(2~{S})-3-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-2-[[3-(2-hydroxyphenyl)-1,2-oxazol-5-yl]methyl]-3-oxidanylidene-propyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic acid(Non-covalent)

62S.5: 24 residues within 4Å: Chain A: D.198, E.200, P.333, G.334, A.335, M.336, E.337, W.363, R.366, V.367, H.370, E.371, H.374, E.393, K.397, E.400, Q.447, F.450, Y.455, Y.892 Ligands: EDO.20, EDO.21, EDO.22, ZN.23 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.363, A:W.363, A:R.366, A:V.367, A:Y.455, A:Y.892, A:Y.892, A:Y.892 Hydrogen bonds: A:G.334, A:A.335, A:E.337, A:E.393, A:K.397, A:Y.455 Water bridges: A:R.366, A:Y.892 pi-Stacking: A:H.370, A:F.450

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

NAG.6: 3 residues within 4Å: Chain A: N.431, K.545, E.936 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.431, A:K.545 NAG.7: 1 residues within 4Å: Chain A: N.294 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain A: N.103 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain A: N.119, D.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.119, A:D.167

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.11: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.2, MES.13 No protein-ligand interaction detected (PLIP)

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

PGE.12: 3 residues within 4Å: Chain A: D.79, K.96, K.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.223

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.13: 3 residues within 4Å: Chain A: I.316, S.486 Ligands: PEG.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.486

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

EDO.14: 1 residues within 4Å: Chain A: Q.544 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.544 EDO.15: 4 residues within 4Å: Chain A: R.578, Q.581, Y.584, K.608 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.578, A:Y.584 EDO.17: 6 residues within 4Å: Chain A: K.354, W.777, N.785, I.786, Y.795, E.820 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.354, A:K.354, A:I.786, A:I.786 EDO.19: 2 residues within 4Å: Chain A: A.857, M.896 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.857 EDO.20: 5 residues within 4Å: Chain A: S.359, L.362, W.363, R.366 Ligands: 62S.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.359, A:R.366 EDO.21: 5 residues within 4Å: Chain A: A.332, G.334, R.345, Y.892 Ligands: 62S.5 No protein-ligand interaction detected (PLIP) EDO.22: 4 residues within 4Å: Chain A: K.397, F.450, D.451 Ligands: 62S.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.451

1 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.16: 2 residues within 4Å: Chain A: D.678, T.954 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.678, A:D.678

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.18: 3 residues within 4Å: Chain A: W.880, L.884, Q.924 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.924

1 x ZN: ZINC ION(Non-covalent)

ZN.23: 5 residues within 4Å: Chain A: H.370, H.374, E.393, Y.455 Ligands: 62S.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpakali, A. et al., Inhibitor-Dependent Usage of the S1' Specificity Pocket of ER Aminopeptidase 2. Acs Med.Chem.Lett. (2022)

Release Date

2022-01-26

Peptides

Endoplasmic reticulum aminopeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoplasmic reticulum aminopeptidase 2

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