SMTL ID : 5xfe.1

Luciferin-regenerating enzyme solved by SAD using XFEL (refined against 11,000 patterns)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

2 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 4 residues within 4Å: Chain A: F.42, C.55, W.87 Ligands: HG.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.55, H2O.7 HG.2: 4 residues within 4Å: Chain A: F.42, C.55, W.87 Ligands: HG.1 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.21, N.163, D.215 Ligands: MPD.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.21, A:D.215, H2O.1, H2O.2, H2O.5

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 5 residues within 4Å: Chain A: L.134, N.163, D.215, F.230 Ligands: MG.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.134, A:F.230, A:F.230 Hydrogen bonds: A:N.163 Water bridges: A:T.37, A:T.37, A:D.215, A:D.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamashita, K. et al., Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography. IUCrJ (2017)

Release Date

2017-08-30

Peptides

Luciferin regenerating enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Luciferin regenerating enzyme

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