SMTL ID : 6q2m.1 (2 other biounits)

Crystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: V.521, V.522, F.523 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.523, A:F.523

2 x DYD: (2S,5S)-hexane-2,5-diol(Non-covalent)

DYD.2: 6 residues within 4Å: Chain A: D.24, G.25, T.26, D.192, R.193, D.194 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.24, A:R.193 Hydrogen bonds: A:G.25 Water bridges: A:E.29, A:F.191 DYD.3: 4 residues within 4Å: Chain A: N.55, R.266, D.284, Y.285 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.285 Hydrogen bonds: A:N.55, A:R.266

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

EDO.4: 1 residues within 4Å: Chain A: K.135 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: D.162, Y.163, Q.164, G.165 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: N.234, Q.235, Q.288, E.316 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: K.326, G.329, E.330, G.340, I.341, P.364 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: D.307, Y.309, D.310 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: N.390, Q.391, R.392 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: R.74, H.176 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: N.89, V.245, V.246, P.247, M.270 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: N.115, E.116 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: G.180, N.182, D.185 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: R.218, G.399, I.402, M.403 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: F.373, E.375, R.398, G.399 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: L.464, Q.465, H.466, P.467, I.469, E.493 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: Y.75, G.76, L.77, H.81, Q.152 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: S.204, L.347, E.349, L.416, S.425, R.442 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: Q.92, D.158, S.159, K.160 Ligand excluded by PLIP

1 x SLU: 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE(Non-covalent)

SLU.20: 22 residues within 4Å: Chain A: S.204, H.250, G.251, F.252, T.256, S.319, G.320, G.321, A.322, P.323, Q.343, G.344, Y.345, G.346, L.347, T.348, S.352, A.353, V.367, D.427, R.442, K.534 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.252, A:T.256, A:A.353 Hydrogen bonds: A:S.204, A:S.319, A:G.321, A:Q.343, A:Y.345, A:G.346, A:T.348, A:T.348, A:T.348, A:A.353, A:D.427, A:R.442, A:K.534 Water bridges: A:L.324 Salt bridges: A:H.250, A:K.534 pi-Stacking: A:F.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Branchini, B.R. et al., Mutagenesis and Structural Studies Reveal the Basis for the Activity and Stability Properties That Distinguish thePhotinusLuciferasesscintillansandpyralis. Biochemistry (2019)

Release Date

2019-10-16

Peptides

Luciferin 4-monooxygenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Luciferin 4-monooxygenase

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