SMTL ID : 3cvv.1

Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion and F0 cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: G.10, C.11 Chain B: G.6, C.7 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.441, C:R.444 EDO.2: 5 residues within 4Å: Chain B: A.9, C.10 Chain C: Q.441, Y.442, F.443 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.441, C:F.443 EDO.5: 4 residues within 4Å: Chain C: W.481, K.482, R.502, E.507 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.482, C:R.502 Water bridges: C:R.502 EDO.6: 3 residues within 4Å: Chain C: H.460, R.463, K.464 No protein-ligand interaction detected (PLIP)

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

FAD.3: 30 residues within 4Å: Chain A: T.8 Chain C: F.267, K.269, T.281, T.282, V.283, L.284, S.285, L.288, L.319, Q.322, L.323, W.325, R.326, Y.329, W.385, H.388, R.391, H.392, A.395, F.414, L.418, D.420, Q.421, D.422, L.425, N.426, N.429, W.430, L.433 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:R.391, C:A.395, C:F.414, C:F.414, C:N.429, C:W.430, C:L.433 Hydrogen bonds: C:K.269, C:T.281, C:T.282, C:V.283, C:L.284, C:S.285, C:S.285, C:H.388, C:R.391, C:D.420, C:D.422, C:N.429, C:N.429 Water bridges: C:H.388 Salt bridges: C:K.269, C:K.269 pi-Cation interactions: C:R.391

1 x FO1: 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol(Non-covalent)

FO1.4: 21 residues within 4Å: Chain C: R.36, K.37, F.67, I.68, L.69, D.70, I.73, W.76, M.77, V.79, R.83, W.84, L.87, D.133, E.135, Y.137, S.138, R.141, K.289, F.290, Q.421 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:F.67, C:I.73, C:V.79, C:W.84, C:L.87, C:F.290 Hydrogen bonds: C:I.68, C:D.70, C:R.83, C:R.83, C:S.138, C:R.141, C:R.141, C:K.289, C:Q.421 Water bridges: C:I.68, C:E.135, C:K.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glas, A.F. et al., The archaeal cofactor F0 is a light-harvesting antenna chromophore in eukaryotes. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-06-16

Peptides

RE11660p: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

RE11660p

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