SMTL ID : 6yi1.2 (1 other biounit)

Crystal structure of human glutaminyl cyclase in complex with Glu(gamma-hydrazide)-Phe-Ala

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x ORT- PHE- ALA- NH2: Glu(gamma-hydrazide)-Phe-Ala(Non-covalent)

ORT-PHE-ALA-NH2.1: 14 residues within 4Å: Chain A: H.108, D.127, E.169, E.170, W.175, D.216, L.217, V.270, I.271, Q.272, W.297, H.298 Ligands: ZN.3, PEG.18 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.175 Hydrogen bonds: A:E.169, A:E.169, A:D.216, A:Q.272, A:Q.272

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

SO4.2: 4 residues within 4Å: Chain A: F.114, S.115, H.116 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.116 Salt bridges: A:H.116 SO4.8: 2 residues within 4Å: Chain A: R.65, R.140 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.62 Salt bridges: A:R.65, A:R.140 SO4.9: 4 residues within 4Å: Chain A: R.120, M.300, N.303, E.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.300, A:N.303 Salt bridges: A:R.120 SO4.10: 3 residues within 4Å: Chain A: K.8, N.9 Ligands: ZN.5 6 PLIP interactions: 6 interactions with chain A Water bridges: A:P.5, A:K.8, A:K.8, A:N.9, A:N.9 Salt bridges: A:K.8 SO4.11: 4 residues within 4Å: Chain A: G.1, P.2, A.3, W.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.3, A:W.4 SO4.19: 5 residues within 4Å: Chain A: P.2, G.199, A.200, R.201, G.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.201, A:G.202 Salt bridges: A:R.201 SO4.22: 5 residues within 4Å: Chain A: Q.240, R.260, Q.263, N.264, Y.265 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.240, A:N.264, A:N.264, A:Y.265 Salt bridges: A:R.260

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.127, E.170, H.298 Ligands: ORT-PHE-ALA-NH2.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.127, A:D.127, A:E.170, A:E.170, A:H.298 ZN.4: 3 residues within 4Å: Chain A: E.44, H.116 Ligands: SO4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.44, A:E.44, A:H.116, H2O.1, H2O.7 ZN.5: 2 residues within 4Å: Chain A: K.8 Ligands: SO4.10 No protein-ligand interaction detected (PLIP) ZN.6: 3 residues within 4Å: Chain A: D.75, H.186, K.190 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.75, A:H.186, H2O.6 ZN.7: 2 residues within 4Å: Chain A: H.244, E.248 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.244, A:E.248, H2O.1, H2O.7

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 11 residues within 4Å: Chain A: A.99, K.100, R.101, H.102, Q.162, M.191, H.196, Q.205, G.208, M.209 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.100, A:Q.162, A:Q.162 Water bridges: A:Q.205 GOL.13: 2 residues within 4Å: Chain A: N.119, V.121 No protein-ligand interaction detected (PLIP) GOL.14: 6 residues within 4Å: Chain A: E.73, I.92, Q.162, K.190, Q.205 Ligands: GOL.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.94, A:T.94, A:Q.205, A:Q.205 Water bridges: A:E.73, A:Q.162

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.15: 3 residues within 4Å: Chain A: P.82, Y.83, L.173 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.83 PGE.16: 4 residues within 4Å: Chain A: H.174, S.176, P.177, Q.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.178

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 3 residues within 4Å: Chain A: R.185, P.277, R.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.185 Water bridges: A:R.281 PEG.18: 7 residues within 4Å: Chain A: W.175, S.176, P.177, S.180, L.181, Q.272 Ligands: ORT-PHE-ALA-NH2.1 No protein-ligand interaction detected (PLIP)

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.20: 4 residues within 4Å: Chain A: H.247, S.256, L.257, E.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.257, A:E.258 Salt bridges: A:H.247 MES.21: 8 residues within 4Å: Chain A: D.69, V.71, N.96, P.97, T.98, A.99, T.151, K.156 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.96, A:T.98, A:A.99, A:T.151 Water bridges: A:D.69, A:D.69, A:N.96, A:T.151 Salt bridges: A:D.69, A:K.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kupski, O. et al., Hydrazides Are Potent Transition-State Analogues for Glutaminyl Cyclase Implicated in the Pathogenesis of Alzheimer's Disease. Biochemistry (2020)

Release Date

2020-07-01

Peptides

Glutaminyl-peptide cyclotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glutaminyl-peptide cyclotransferase

Related Entries With Identical Sequence