SMTL ID : 4cdm.1

Crystal structure of M. mazei photolyase soaked with synthetic 8-HDF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: Y.270, L.282, S.283, N.284, L.285, S.286, L.289, F.316, E.319, I.320, W.323, K.324, S.327, K.390, G.393, R.396, M.397, A.400, N.421, D.427, G.428, D.430, N.432, G.433, G.436, I.437, S.440 Ligands: GOL.8 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:R.396, A:A.400 Hydrogen bonds: A:Y.270, A:S.283, A:N.284, A:N.284, A:L.285, A:S.286, A:S.286, A:E.319, A:E.319, A:R.396, A:N.421, A:D.427, A:D.427, A:N.432 Salt bridges: A:K.390 pi-Cation interactions: A:R.396, A:R.396

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)

FO1.2: 16 residues within 4Å: Chain A: M.43, S.44, R.45, Q.47, F.73, C.74, L.75, T.76, M.90, S.136, K.141, W.144, H.290, F.291, G.428, R.429 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:C.74, A:T.76, A:S.136, A:K.141, A:R.429, A:R.429 Water bridges: A:R.45, A:C.74

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

SO4.3: 6 residues within 4Å: Chain A: I.84, R.85, R.233, A.234, F.243, R.423 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.84, A:R.85, A:A.234 Salt bridges: A:R.85, A:R.423 SO4.4: 6 residues within 4Å: Chain A: N.309, P.310, G.311, S.312, K.313, K.314 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.311, A:K.314 SO4.5: 5 residues within 4Å: Chain A: K.467, F.470, D.471, V.472, K.473 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.470, A:D.471, A:V.472, A:K.473 Salt bridges: A:K.467 SO4.6: 5 residues within 4Å: Chain A: Q.95, E.98, T.217, L.218, S.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.95, A:L.218, A:S.219, A:S.219

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: A.178, H.179, R.182, W.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.179, A:H.179, A:R.182 GOL.8: 5 residues within 4Å: Chain A: W.323, M.397, G.436, W.439 Ligands: FAD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiontke, S. et al., Structural and Evolutionary Aspects of Antenna Chromophore Usage by Class II Photolyases. J.Biol.Chem. (2014)

Release Date

2014-05-21

Peptides

DEOXYRIBODIPYRIMIDINE PHOTOLYASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DEOXYRIBODIPYRIMIDINE PHOTOLYASE

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