SMTL ID : 2xrz.1 (1 other biounit)

X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei in complex with intact CPD-lesion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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 Chain B: N.7 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:R.396, A:A.400 Hydrogen bonds: A:Y.270, A:Y.270, A:S.283, A:N.284, A:L.285, A:S.286, A:S.286, A:R.396, A:N.421, A:D.427, A:N.432 Water bridges: A:R.396, A:R.396, A:Y.434 Salt bridges: A:K.390 pi-Cation interactions: A:R.396, A:R.396

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

SO4.2: 7 residues within 4Å: Chain A: G.83, I.84, R.85, R.233, A.234, F.243, R.423 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.84, A:R.85, A:A.234 Water bridges: A:F.243, A:R.423 Salt bridges: A:R.85, A:R.423

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: F.248, N.280, L.282, N.284, E.384, T.388, K.390, H.392, Y.479 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.280, A:N.284, A:E.384, A:T.388, A:K.390, A:Y.479 Water bridges: A:K.390, A:M.391 GOL.4: 6 residues within 4Å: Chain A: Y.176, P.344, S.345, W.346 Chain C: C.10, C.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.345, A:W.346 Water bridges: A:S.345 GOL.5: 5 residues within 4Å: Chain A: S.44, Q.47, C.74, E.78, W.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.47, A:C.74 Water bridges: A:W.42, A:C.74

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: R.139, D.338, I.418, Y.434 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.338, A:I.418, A:Y.434 Hydrogen bonds: A:R.139, A:D.338 Water bridges: A:Y.434 ACT.7: 7 residues within 4Å: Chain A: K.401, K.402, E.405, T.455, R.459, Y.460, M.461 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.401, A:T.455 Hydrogen bonds: A:M.461 Salt bridges: A:K.402 ACT.8: 4 residues within 4Å: Chain A: Q.95, E.98, L.218, S.219 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.95, A:E.98, A:L.218, A:S.219 Water bridges: A:E.98 ACT.9: 6 residues within 4Å: Chain A: R.274, A.315, D.318, E.319, W.323 Chain B: N.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.315 Hydrogen bonds: A:D.318, A:E.319 Water bridges: A:R.182 Salt bridges: A:R.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiontke, S. et al., Crystal Structures of an Archaeal Class II DNA Photolyase and its Complex with Uv-Damaged Duplex DNA. Embo J. (2011)

Release Date

2011-09-14

Peptides

DEOXYRIBODIPYRIMIDINE PHOTOLYASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DEOXYRIBODIPYRIMIDINE PHOTOLYASE

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