SMTL ID : 7pfs.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

3 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.1: 6 residues within 4Å: Chain A: N.219, T.255, T.256, V.257, K.258, Y.487 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.487 NAG-NAG-BMA.2: 12 residues within 4Å: Chain A: H.83, P.84, N.85, T.87, R.226, E.227, G.246, L.248 Chain B: H.272, P.290, D.291, R.293 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.293, A:G.246, B:R.293, B:R.293 Hydrophobic interactions: B:P.290 NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: N.405, K.466 No protein-ligand interaction detected (PLIP)

5 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: 4 residues within 4Å: Chain A: N.431, K.545, L.580, E.582 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: N.219, T.255, T.256, V.257, K.258, Y.487 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.431 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.405, D.414, K.466 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.5: 14 residues within 4Å: Chain A: H.272, S.273, L.274, P.290, D.291, R.293 Chain B: H.83, P.84, N.85, T.87, R.226, E.227, G.246, L.248 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.293, A:R.293, B:G.246, A:R.293, A:R.293, A:S.273 Hydrophobic interactions: A:P.290 Water bridges: A:H.272, A:R.293

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

NAG.10: 3 residues within 4Å: Chain A: N.650, T.652, L.653 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain A: N.103 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: N.119, D.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.119 NAG.13: 1 residues within 4Å: Chain A: N.714 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.714 NAG.14: 2 residues within 4Å: Chain A: N.294, D.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.294 NAG.22: 1 residues within 4Å: Chain B: N.650 No protein-ligand interaction detected (PLIP) NAG.23: 1 residues within 4Å: Chain B: N.714 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain B: N.119, E.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.136

2 x 7OO: [(2~{S})-3-[[(2~{S})-1-azanyl-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-2-[(3,5-diphenylphenyl)methyl]-3-oxidanylidene-propyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic acid(Non-covalent)

7OO.15: 22 residues within 4Å: Chain A: E.200, P.201, A.332, P.333, G.334, A.335, M.336, E.337, R.345, W.363, H.370, E.371, H.374, E.393, Q.447, F.450, D.451, E.452, Y.455, N.456, Y.892 Ligands: ZN.20 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.333, A:W.363, A:Y.455, A:Y.892, A:Y.892 Hydrogen bonds: A:E.200, A:A.335, A:E.337, A:E.337, A:Y.455 pi-Stacking: A:F.450 7OO.21: 22 residues within 4Å: Chain B: E.200, P.201, A.332, P.333, G.334, A.335, M.336, E.337, R.345, W.363, H.370, E.371, H.374, E.393, Q.447, F.450, D.451, E.452, Y.455, N.456, Y.892 Ligands: ZN.25 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:E.200, B:W.363, B:E.452, B:Y.455, B:Y.455, B:Y.892 Hydrogen bonds: B:A.332, B:G.334, B:A.335, B:E.337, B:E.337, B:E.371, B:H.374, B:Y.455, B:Y.455 pi-Stacking: B:F.450, B:Y.455

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

EDO.16: 4 residues within 4Å: Chain A: D.90, Q.169, A.170, K.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.90 EDO.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.18: 3 residues within 4Å: Chain A: Q.544, R.583, Y.584 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.544, A:R.583

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.19: 1 residues within 4Å: Chain A: H.77 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.20: 5 residues within 4Å: Chain A: H.370, H.374, E.393, Y.455 Ligands: 7OO.15 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393, A:E.393 ZN.25: 4 residues within 4Å: Chain B: H.370, H.374, E.393 Ligands: 7OO.21 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.370, B:H.374, B:E.393, B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Endoplasmic reticulum aminopeptidase 2

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