SMTL ID : 5ab2.2 (1 other biounit)

Crystal structure of aminopeptidase ERAP2 with ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

monomer

Ligands

1 x GLY- PRO- GLY- ARG- ALA- PHE: GPI(Non-covalent)

GLY-PRO-GLY-ARG-ALA-PHE.1: 20 residues within 4Å: Chain A: E.200, P.333, G.334, A.335, M.336, E.337, R.345, D.360, W.363, H.370, E.371, H.374, E.393, F.450, D.451, E.452, Y.455, N.456, Y.892 Ligands: ZN.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.892 Hydrogen bonds: A:G.334, A:E.337, A:F.450, A:N.456 Salt bridges: A:E.452 pi-Stacking: A:W.363, A:W.363 pi-Cation interactions: A:Y.455

1 x NAG- NAG- BMA- BMA: beta-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-BMA.2: 4 residues within 4Å: Chain A: N.85, S.88, E.227, L.248 No protein-ligand interaction detected (PLIP)

2 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.650, L.653 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 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:V.257

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

NAG.5: 1 residues within 4Å: Chain A: N.103 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: N.405, K.466, E.471 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.405, A:K.466, A:E.471 NAG.7: 2 residues within 4Å: Chain A: N.431, K.545 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.431, A:K.545

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 6 residues within 4Å: Chain A: E.337, H.370, H.374, E.393 Ligands: GLY-PRO-GLY-ARG-ALA-PHE.1, GLY-PRO-GLY-ARG-ALA-PHE.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393, A:E.393

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

EDO.9: 2 residues within 4Å: Chain A: K.483, K.484 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.483 EDO.10: 2 residues within 4Å: Chain A: M.778, E.779 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain A: E.772, Q.776 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.772, A:Q.776

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpakali, A. et al., Structural Basis for Antigenic Peptide Recognition and Processing by Endoplasmic Reticulum (Er) Aminopeptidase 2. J.Biol.Chem. (2015)

Release Date

2015-09-30

Peptides

ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2

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