SMTL ID : 6m8p.7 (21 other biounits)

Human ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.31 Å

Oligo State

monomer

Ligands

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.1: 5 residues within 4Å: Chain A: H.52, A.53, N.54, E.194, L.215 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 1 residues within 4Å: Chain A: N.138 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: E.304, H.337, H.341, E.360 Ligands: P52.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.337, A:H.341, A:E.360, A:E.360

1 x P52: Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide(Non-covalent)

P52.4: 20 residues within 4Å: Chain A: Q.165, E.167, Q.299, S.300, G.301, A.302, M.303, E.304, T.334, H.337, E.338, H.341, E.360, K.364, E.367, F.417, Y.422, S.828, S.829 Ligands: ZN.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.167, A:Q.299, A:F.417 Hydrogen bonds: A:G.301, A:A.302, A:E.360, A:E.360, A:Y.422, A:Y.422, A:S.828 pi-Stacking: A:F.417

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: T.674, W.675, R.705 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.675 Salt bridges: A:R.705 SO4.6: 4 residues within 4Å: Chain A: L.158, R.159, I.160, R.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.160 Salt bridges: A:R.196 SO4.7: 4 residues within 4Å: Chain A: Y.151, R.152, K.757, K.787 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.152 Salt bridges: A:K.259, A:K.757, A:K.787 SO4.8: 5 residues within 4Å: Chain A: I.640, Y.643, K.644, R.766, R.800 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.643 Salt bridges: A:K.644, A:R.766, A:R.800 SO4.9: 3 residues within 4Å: Chain A: R.499, E.552, E.553 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.553, A:E.553 Salt bridges: A:R.499 SO4.10: 3 residues within 4Å: Chain A: R.497, N.500, H.502 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.500 Salt bridges: A:H.502 SO4.11: 3 residues within 4Å: Chain A: R.649, D.650, M.651 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.650 Salt bridges: A:R.649 SO4.12: 2 residues within 4Å: Chain A: Q.810, R.813 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.813 SO4.13: 6 residues within 4Å: Chain A: T.588, V.590, S.591, S.592, R.595, E.628 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.592, A:S.592 Salt bridges: A:R.595 SO4.14: 5 residues within 4Å: Chain A: R.312, Q.789, P.792, S.829, H.832 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.299 Salt bridges: A:R.312, A:H.832 SO4.15: 2 residues within 4Å: Chain A: K.65, R.92 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.65, A:R.92 SO4.16: 2 residues within 4Å: Chain A: N.817, K.818 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.817 SO4.17: 3 residues within 4Å: Chain A: R.192, V.211, A.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.212 Salt bridges: A:R.192 SO4.18: 2 residues within 4Å: Chain A: H.537, R.538 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.538, A:R.538 SO4.20: 1 residues within 4Å: Chain A: K.532 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.532

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.19: 1 residues within 4Å: Chain A: N.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.398, A:N.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maben, Z. et al., Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nat Commun (2021)

Release Date

2019-12-18

Peptides

Endoplasmic reticulum aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

Endoplasmic reticulum aminopeptidase 1

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