SMTL ID : 7ayv.1

X-ray crystallographic structure of (6-4)photolyase from Drosophila melanogaster at cryogenic temperature

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: W.302, Y.306, H.365, H.369, N.406, W.409 Ligands: FAD.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.306, A:Y.306, A:H.365

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 30 residues within 4Å: Chain A: F.244, K.246, T.258, T.259, V.260, L.261, S.262, L.265, L.296, Q.299, L.300, W.302, R.303, Y.306, W.362, H.365, R.368, H.369, A.372, F.391, L.395, D.397, Q.398, D.399, L.402, N.403, N.406, W.407, L.410 Ligands: GOL.1 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:R.368, A:A.372, A:F.391, A:F.391, A:N.406, A:W.407, A:L.410 Hydrogen bonds: A:K.246, A:T.258, A:T.259, A:T.259, A:V.260, A:L.261, A:S.262, A:S.262, A:H.365, A:R.368, A:D.397, A:D.397, A:D.399, A:N.406, A:N.406 Water bridges: A:S.262, A:H.365 Salt bridges: A:K.246, A:K.246 pi-Cation interactions: A:R.368, A:R.368

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

SO4.3: 3 residues within 4Å: Chain A: W.458, R.479 Ligands: SO4.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.479 SO4.4: 7 residues within 4Å: Chain A: Y.347, W.458, R.479, K.482, H.483, E.484 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.347, A:E.484 Salt bridges: A:R.479 SO4.5: 5 residues within 4Å: Chain A: W.458, L.472, H.478, R.479, K.482 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.479, A:R.479 Salt bridges: A:H.478, A:R.479, A:K.482 SO4.6: 4 residues within 4Å: Chain A: H.333, P.334, D.335, H.336 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.335, A:D.335, A:H.336 Salt bridges: A:H.333, A:H.336 SO4.7: 2 residues within 4Å: Chain A: R.5, R.37 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.5, A:R.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cellini, A. et al., The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature. Acta Crystallogr D Struct Biol (2021)

Release Date

2021-08-18

Peptides

RE11660p: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RE11660p