SMTL ID : 1tez.1 (3 other biounits)

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x DC- DG- DA- DA- DG- DC- DC- DG- DA: 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'(Non-covalent)

DC-DG-DA-DA-DG-DC-DC-DG-DA.1: 22 residues within 4Å: Chain A: A.1, T.2, C.3, G.4, G.5, C.6 Chain B: S.139, G.140, Y.145, S.146, V.147, P.150, D.398, P.399, K.400, P.401, L.402, Y.467, K.471 Ligands: C.3, G.4, MG.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.285, B:W.285 Hydrogen bonds: B:Y.148, B:G.149, B:R.231 pi-Stacking: B:W.285

1 x TCP: 5'-METHYLTHYMIDINE(Non-covalent)

TCP.2: 7 residues within 4Å: Chain A: T.7 Chain B: N.348, R.349, M.352, W.391 Ligands: C.3, FAD.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.391, B:W.391 Hydrogen bonds: B:N.348, B:N.348, B:R.349, B:R.349 Water bridges: B:R.231, B:R.231 pi-Stacking: B:W.391

2 x C: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C.3: 8 residues within 4Å: Chain B: R.349, F.405, Q.410, F.414 Ligands: DC-DG-DA-DA-DG-DC-DC-DG-DA.1, DC-DG-DA-DA-DG-DC-DC-DG-DA.1, TCP.2, G.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.406, B:N.406, B:Q.410, B:Q.460 Water bridges: B:R.349, B:R.349 Salt bridges: B:R.349, B:K.413, B:K.413 C.5: 3 residues within 4Å: Chain B: N.406, Q.460 Ligands: G.4 Protein-ligand interaction information (PLIP) not available

1 x G: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

G.4: 9 residues within 4Å: Chain B: I.404, F.405, N.406, Q.410, Q.460 Ligands: DC-DG-DA-DA-DG-DC-DC-DG-DA.1, DC-DG-DA-DA-DG-DC-DC-DG-DA.1, C.3, C.5 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain B: D.398 Ligands: DC-DG-DA-DA-DG-DC-DC-DG-DA.1 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.398, H2O.1, H2O.1, H2O.17, H2O.17

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

FAD.7: 29 residues within 4Å: Chain A: T.7 Chain B: Y.227, T.239, S.240, G.241, L.242, S.243, L.246, W.279, E.282, L.283, R.286, Y.289, W.345, M.346, N.348, R.351, M.352, A.355, F.373, L.377, D.379, G.380, D.381, A.384, N.385, G.388, W.389 Ligands: TCP.2 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:R.351, B:A.355, B:F.373, B:W.389 Hydrogen bonds: B:Y.227, B:S.240, B:G.241, B:L.242, B:S.243, B:E.282, B:N.348, B:R.351, B:D.379, B:D.381 Water bridges: B:T.239, B:Y.289, B:N.348 pi-Cation interactions: B:R.351

1 x HDF: 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE(Non-covalent)

HDF.8: 16 residues within 4Å: Chain B: R.9, F.34, C.35, L.36, D.37, I.40, L.41, M.46, R.50, L.54, D.100, E.102, G.105, R.108, K.247, F.248 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.34, B:I.40, B:I.40, B:L.41, B:L.54, B:F.248, B:F.248 Hydrogen bonds: B:C.35, B:D.37, B:R.50, B:E.102, B:G.105, B:R.108, B:R.108, B:K.247 Water bridges: B:C.35, B:D.37, B:R.50, B:E.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mees, A. et al., Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science (2004)

Release Date

2004-12-14

Peptides

Deoxyribodipyrimidine photolyase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

Deoxyribodipyrimidine photolyase

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