SMTL ID : 6ryf.1

High-resolution crystal structure of ERAP1 in complex with 15mer phosphinic peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 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: 5 residues within 4Å: Chain A: H.54, Q.56, A.107, G.108, N.109 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: H.23, A.24, N.25, E.165, E.184, L.186 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.184

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.308, H.312, E.331, Y.393 Chain B: X.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.308, A:H.312, A:E.331, A:E.331

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.4: 17 residues within 4Å: Chain A: G.357, F.360, D.361, E.364, K.506, N.596, S.603, Q.630, N.633, E.634, P.637, M.638, L.641, N.873, W.876 Chain B: V.12 Ligands: EDO.9 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:F.360, A:D.361, A:K.506, A:K.506, A:N.596, A:S.603, A:Q.630, A:P.637 Water bridges: A:F.360, A:E.364, A:K.506, A:S.603, A:S.603, A:Q.630, A:W.876

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

EDO.5: 11 residues within 4Å: Chain A: H.53, E.84, H.115, T.140, A.141, R.143, M.144, P.381, R.385, E.820 Ligands: EDO.18 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: N.325, D.326, S.375, T.376, P.377, L.481 Ligand excluded by PLIP EDO.7: 10 residues within 4Å: Chain A: H.372, T.376, P.377, V.378, Q.383, E.386, M.387, R.861 Ligands: EDO.24, EDO.25 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: S.295, A.296, S.297, R.680, M.681, S.684, D.721 Chain B: R.9 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: E.364, L.368, K.506, T.869, E.872 Ligands: B3P.4 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: R.809, K.810, F.849 Ligands: EDO.23 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: W.737, D.738, K.768, W.771 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: E.322, K.426, N.427, T.428 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: N.5, K.6, I.7, R.8, E.379 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain A: F.289, D.290, A.291, E.292, K.293, S.294, D.673, R.680, V.720 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: E.502, H.503, Y.504, M.505, I.604, K.606 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: Q.669, T.670, W.671, T.672, R.701 Ligand excluded by PLIP EDO.17: 10 residues within 4Å: Chain A: P.139, T.140, R.143, D.150, E.151, P.152, S.198, T.199, Y.200, W.324 Ligand excluded by PLIP EDO.18: 10 residues within 4Å: Chain A: I.7, H.51, R.82, Q.83, E.84, R.143, E.379, N.380, P.381 Ligands: EDO.5 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: K.644, R.645, D.646, T.839 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain A: H.23, A.24, N.25, T.28, T.30, F.31, W.32 Ligands: NAG-NAG.2 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: D.614, W.887, S.890, E.891, K.892, L.893 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: R.493, G.494, R.495, N.496, I.545, E.549 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: R.809, K.810, W.812, N.813, F.849, L.853 Ligands: EDO.10 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: P.377, V.378, E.379, Q.383 Ligands: EDO.7 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: S.371, H.372, P.373, T.376, K.483, R.861 Ligands: EDO.7 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.26: 4 residues within 4Å: Chain A: H.53, H.54, L.55, M.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.144 NA.27: 7 residues within 4Å: Chain A: K.395, T.478, W.479, Q.482, K.483, G.484, W.518 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.395, A:K.483 NA.28: 9 residues within 4Å: Chain A: D.366, S.371, H.372, P.373, V.374, V.391, K.395, K.483, G.484 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.371, A:V.374, A:K.395, A:K.395, A:G.484 NA.29: 5 residues within 4Å: Chain A: V.602, S.608, I.609, K.879, N.880 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.609, A:N.880 Water bridges: A:K.879

1 x PPI: PROPANOIC ACID(Non-covalent)

PPI.30: 4 residues within 4Å: Chain A: M.531, V.532, H.533, R.534 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.534 Hydrogen bonds: A:R.534, A:R.534 Salt bridges: A:H.533

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

NAG.31: 1 residues within 4Å: Chain A: N.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.369, A:N.369 NAG.32: 1 residues within 4Å: Chain A: N.715 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.715

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giastas, P. et al., Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-12-18

Peptides

Endoplasmic reticulum aminopeptidase 1: A
PSE-ARG-ILE-GLN-ARG-ALA-PHE-VAL-THR-ILE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

Endoplasmic reticulum aminopeptidase 1

PSE-ARG-ILE-GLN-ARG-ALA-PHE-VAL-THR-ILE