SMTL ID : 4cdn.1 (1 other biounit)

Crystal structure of M. mazei photolyase with its in vivo reconstituted 8-HDF antenna chromophore

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:R.396, A:A.400, A:I.437 Hydrogen bonds: A:Y.270, A:Y.270, A:S.283, A:N.284, A:L.285, A:S.286, A:S.286, A:S.286, A:E.319, A:R.396, A:N.421, A:D.427, A:N.432, A:G.433 Water bridges: A:S.327, A:G.393, A:R.396, A:R.396 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: 17 residues within 4Å: Chain A: S.44, R.45, Q.47, F.73, C.74, L.75, T.76, F.79, A.82, Y.87, M.90, S.136, K.141, W.144, H.290, F.291, R.429 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.79, A:A.82, A:Y.87 Hydrogen bonds: A:S.44, A:C.74, A:T.76, A:S.136, A:R.429, A:R.429 Water bridges: A:R.45, A:C.74, A:H.290 pi-Stacking: A:F.79, A:F.79

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: L.282, N.284, E.384, T.388, K.390, H.392 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.284, A:T.388, A:K.390 Water bridges: A:N.284, A:N.284, A:G.393 GOL.4: 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 Water bridges: A:W.323 GOL.5: 3 residues within 4Å: Chain A: P.190, E.191, E.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.194

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

SO4.6: 4 residues within 4Å: Chain A: A.177, A.178, H.179, R.182 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.178, A:H.179 Water bridges: A:R.182, A:R.182 Salt bridges: A:R.182

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 5 residues within 4Å: Chain A: K.372, T.373, H.374, N.379 Ligands: PEG.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.372, A:N.379 PGE.9: 7 residues within 4Å: Chain A: L.14, S.31, G.32, K.33, Q.34, P.155, F.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.32, A:Q.34

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 8 residues within 4Å: Chain A: N.238, D.240, P.241, L.242, F.243, A.370, L.386, Y.424 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.238, A:D.240, A:L.242, A:F.243, A:Y.424 Water bridges: A:E.369 PEG.10: 6 residues within 4Å: Chain A: R.359, S.360, E.405, W.406, E.453, V.454 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.360, A:H.361, A:E.405, A:E.405 Water bridges: A:R.452, A:E.453, A:E.453 PEG.11: 6 residues within 4Å: Chain A: D.77, G.113, D.114, P.115, I.140, W.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.77, A:W.144 PEG.12: 5 residues within 4Å: Chain A: H.374, D.375, P.376, Y.463 Ligands: PGE.7 No protein-ligand interaction detected (PLIP)

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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