SMTL ID : 3umv.1 (1 other biounit)

Eukaryotic Class II CPD photolyase structure reveals a basis for improved UV-tolerance in plants

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: W.241, G.283, H.388, K.390 Ligands: URE.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.388 EDO.2: 4 residues within 4Å: Chain A: S.184, H.445, D.446, Q.447 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.445, A:Q.447, A:Q.447 Water bridges: A:A.185, A:A.185, A:D.446, A:D.446, A:R.459 EDO.3: 6 residues within 4Å: Chain A: R.46, L.82, S.138, L.140, V.143, P.431 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.46, A:S.138 Water bridges: A:R.46 EDO.4: 5 residues within 4Å: Chain A: E.360, E.405, R.452, P.453, Y.460 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.360, A:R.452, A:R.452 EDO.5: 2 residues within 4Å: Chain A: D.148, A.149 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.149 EDO.6: 2 residues within 4Å: Chain A: P.78, R.79 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.79, A:R.79, A:R.79, A:T.115, A:R.228, A:R.228, A:E.232, A:E.232

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

FAD.7: 26 residues within 4Å: Chain A: Y.268, L.281, S.282, G.283, L.284, S.285, L.288, F.316, E.319, L.320, R.323, R.324, K.390, G.393, R.396, M.397, A.400, N.421, D.427, G.428, D.430, S.432, G.433, G.436, C.437, S.440 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:R.396, A:A.400 Hydrogen bonds: A:Y.268, A:Y.268, A:S.282, A:G.283, A:L.284, A:S.285, A:S.285, A:R.396, A:N.421, A:D.427, A:S.432 Water bridges: A:G.393, A:R.396, A:R.396, A:S.432 Salt bridges: A:K.390 pi-Cation interactions: A:R.396, A:R.396

5 x URE: UREA(Non-functional Binders)

URE.8: 6 residues within 4Å: Chain A: P.278, E.384, K.390, M.391, H.392 Ligands: EDO.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.278, A:K.390, A:H.392 Water bridges: A:E.384, A:E.384 URE.9: 7 residues within 4Å: Chain A: W.449, K.450, R.452, G.456, I.458, R.459, Y.460 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.450, A:I.458, A:Y.460 Water bridges: A:K.450 URE.10: 4 residues within 4Å: Chain A: V.220, D.221, A.224, L.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.221, A:D.221 URE.11: 6 residues within 4Å: Chain A: F.74, A.75, L.76, F.77, L.82, L.93 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.75, A:F.77 Water bridges: A:L.82, A:R.429 URE.12: 6 residues within 4Å: Chain A: F.112, L.113, F.114, E.215, P.217, E.218 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.113, A:E.215, A:E.215, A:E.218 Water bridges: A:L.113, A:L.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hitomi, K. et al., Eukaryotic Class II Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals Basis for Improved Ultraviolet Tolerance in Plants. J.Biol.Chem. (2012)

Release Date

2011-12-21

Peptides

Deoxyribodipyrimidine photo-lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Deoxyribodipyrimidine photo-lyase

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