SMTL ID : 6muj.4 (4 other biounits)

Formylglycine generating enzyme bound to copper

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x GLY: GLYCINE(Non-covalent)

GLY.1: 3 residues within 4Å: Chain A: D.311, T.313, S.314 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.313

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.24, P.25, S.27, W.160, A.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.76 Water bridges: A:R.24, A:S.27

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: N.199, I.200, D.213, H.215 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.200, A:D.213, A:H.215, H2O.2, H2O.2

5 x CU: COPPER (II) ION(Non-covalent)

CU.4: 4 residues within 4Å: Chain A: W.239, C.277, C.282, R.284 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.277, A:C.282, A:C.282 CU.5: 4 residues within 4Å: Chain A: H.100, L.101, P.206, H.207 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.100, A:H.207 CU.6: 2 residues within 4Å: Chain A: R.33, H.66 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.66 CU.7: 2 residues within 4Å: Chain A: D.258, H.260 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.258, A:H.260, H2O.1 CU.8: 1 residues within 4Å: Chain A: H.215 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.215, H2O.5

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.9: 4 residues within 4Å: Chain A: A.97, W.120, N.293, S.299 No protein-ligand interaction detected (PLIP)

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 3 residues within 4Å: Chain A: Y.49, Y.281, R.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.284, A:R.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Appel, M.J. et al., Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O2activation. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2019-02-27

Peptides

Formylglycine-generating enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Formylglycine-generating enzyme

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