SMTL ID : 3fy4.1 (2 other biounits)

(6-4) Photolyase Crystal Structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 6 residues within 4Å: Chain A: H.368, R.376, W.408, F.415, R.420, Y.422 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.408, A:Y.422 pi-Stacking: A:H.368, A:F.415 IMD.2: 5 residues within 4Å: Chain A: N.330, D.378, L.379, F.380, K.492 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.330, A:A.485 IMD.3: 4 residues within 4Å: Chain A: F.252, L.253, P.255, W.359 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 11 residues within 4Å: Chain A: K.244, P.245, P.292, V.293, Q.298, W.301, H.364, H.368, N.405, W.408 Ligands: FAD.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.298 Water bridges: A:K.244

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: W.238, N.241, F.242, E.243, K.246, A.256 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.241, A:E.243, A:A.256 Water bridges: A:N.241, A:E.243, A:G.247

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

FAD.6: 31 residues within 4Å: Chain A: F.242, K.244, T.257, T.258, V.259, M.260, S.261, L.264, L.295, Q.298, L.299, W.301, R.302, F.305, W.361, M.362, H.364, R.367, H.368, A.371, F.390, L.394, D.396, S.397, D.398, I.401, N.402, N.405, W.406, L.409 Ligands: MES.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:R.367, A:A.371, A:F.390, A:F.390, A:N.405, A:W.406, A:L.409 Hydrogen bonds: A:T.257, A:T.258, A:V.259, A:M.260, A:S.261, A:H.364, A:H.364, A:R.367, A:D.396, A:D.398, A:N.405 Water bridges: A:K.244, A:K.244, A:S.261 Salt bridges: A:K.244 pi-Cation interactions: A:R.367, A:R.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hitomi, K. et al., Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-04-28

Peptides

6-4 photolyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

6-4 photolyase

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