SMTL ID : 5ab0.1 (1 other biounit)

Crystal structure of aminopeptidase ERAP2 with ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 7 residues within 4Å: Chain A: H.83, P.84, N.85, R.226, E.227, G.246, L.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.246 NAG-NAG.4: 2 residues within 4Å: Chain A: N.650, L.653 No protein-ligand interaction detected (PLIP)

2 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.2: 8 residues within 4Å: Chain A: H.77, N.219, T.255, T.256, V.257, K.258, Y.487 Ligands: MES.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.487 NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: L.401, I.402, N.405, D.414, E.471 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.370, H.374, E.393, Y.455 Chain B: X.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393, A:E.393

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

NAG.6: 2 residues within 4Å: Chain A: S.102, N.103 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: N.431, K.545, L.580 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.431, A:K.545 NAG.8: 4 residues within 4Å: Chain A: T.118, N.119, E.136, D.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.167 Water bridges: A:N.119 NAG.9: 3 residues within 4Å: Chain A: R.712, N.714, Q.869 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.869

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

EDO.10: 3 residues within 4Å: Chain A: H.77, D.79, S.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.221 EDO.11: 5 residues within 4Å: Chain A: S.273, S.275, K.283, S.285, Y.287 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.273, A:S.275, A:S.275, A:K.283, A:S.285

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

MES.12: 2 residues within 4Å: Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.487

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

ENDOPLASMATIC RETICULUM AMINOPEPTIDASE 2: A
DG025: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

ENDOPLASMATIC RETICULUM AMINOPEPTIDASE 2

DG025

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