SMTL ID : 6yi1.1 (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

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

ORT-PHE-ALA-NH2.1: 15 residues within 4Å: Chain A: H.108, D.127, E.169, E.170, W.175, D.216, L.217, Y.267, I.271, Q.272, D.273, F.293, W.297, H.298 Ligands: ZN.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.169, A:E.169, A:D.216, A:Q.272, A:Q.272 Water bridges: A:Y.267 ORT-PHE-ALA-NH2.2: 8 residues within 4Å: Chain A: H.247, E.248, G.250, L.252, K.253, D.254, H.255 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.250, A:D.254, A:D.254 Water bridges: A:G.250

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

SO4.3: 2 residues within 4Å: Chain A: R.260, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.264 Salt bridges: A:R.260 SO4.9: 6 residues within 4Å: Chain A: N.96, P.97, T.98, A.99, T.151, K.156 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.96, A:N.96, A:T.98, A:A.99 Water bridges: A:N.96, A:T.151 SO4.10: 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 SO4.11: 3 residues within 4Å: Chain A: A.200, R.201, G.202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.201, A:G.202 Water bridges: A:T.203 Salt bridges: A:R.201

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.5: 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.8 ZN.6: 2 residues within 4Å: Chain A: D.254 Ligands: ORT-PHE-ALA-NH2.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.254, H2O.1, H2O.7, H2O.9 ZN.7: 3 residues within 4Å: Chain A: H.244, E.248, L.257 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.244, A:E.248, A:E.248, H2O.1 ZN.8: 2 residues within 4Å: Chain A: E.44, H.116 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.44, A:E.44, A:H.116, H2O.2, H2O.8

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain A: N.9, P.230, N.231, R.234 Ligands: PEG.18 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.9 Water bridges: A:N.9, A:N.9, A:P.230, A:N.231, A:N.231 GOL.13: 9 residues within 4Å: Chain A: A.99, K.100, R.101, H.102, Q.162, H.196, Q.205, G.208, M.209 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.100, A:H.102, A:Q.162, A:Q.162

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.14: 4 residues within 4Å: Chain A: L.78, S.79, Q.80, Y.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.80

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.15: 8 residues within 4Å: Chain A: L.16, S.18, L.21, A.241, H.244, E.245, E.248, L.249 No protein-ligand interaction detected (PLIP) PG4.16: 7 residues within 4Å: Chain A: F.228, F.229, P.230, A.233, R.234, E.237, S.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.237, A:E.237 PG4.17: 3 residues within 4Å: Chain A: V.270, L.279, R.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.280

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

PEG.18: 5 residues within 4Å: Chain A: N.9, Y.10, Q.12, R.234 Ligands: GOL.12 No protein-ligand interaction detected (PLIP) PEG.19: 5 residues within 4Å: Chain A: F.114, H.298, T.299, M.300, D.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.300 PEG.20: 4 residues within 4Å: Chain A: Y.46, Y.83, R.86, Y.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.86, A:R.86

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
A

Glutaminyl-peptide cyclotransferase

Related Entries With Identical Sequence