SMTL ID : 2j08.2 (1 other biounit)

Thermus DNA photolyase with 8-Iod-riboflavin antenna chromophore

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-dimer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 1 residues within 4Å: Chain A: H.117 Ligand excluded by PLIP CL.2: 1 residues within 4Å: Chain A: P.148 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: H.117 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain B: P.148 Ligand excluded by PLIP

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

FAD.3: 28 residues within 4Å: Chain A: Y.197, G.209, S.210, R.211, L.212, S.213, F.216, W.241, E.244, L.245, W.247, R.248, S.251, F.307, L.308, S.309, N.310, R.313, M.314, A.317, L.339, D.341, G.342, D.343, V.346, N.347, Q.349, G.350 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:R.313, A:M.314, A:A.317 Hydrogen bonds: A:Y.197, A:S.210, A:R.211, A:L.212, A:S.213, A:S.213, A:R.248, A:R.248, A:N.310, A:N.310, A:R.313, A:R.313, A:D.341, A:D.341, A:D.343, A:N.347, A:Q.349 Water bridges: A:N.310, A:N.310 pi-Cation interactions: A:R.313, A:R.313 FAD.9: 28 residues within 4Å: Chain B: Y.197, G.209, S.210, R.211, L.212, S.213, F.216, W.241, E.244, L.245, W.247, R.248, S.251, F.307, L.308, S.309, N.310, R.313, M.314, A.317, L.339, D.341, G.342, D.343, V.346, N.347, Q.349, G.350 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:R.313, B:M.314, B:A.317 Hydrogen bonds: B:Y.197, B:Y.197, B:S.210, B:R.211, B:L.212, B:S.213, B:S.213, B:E.244, B:R.248, B:R.248, B:N.310, B:N.310, B:R.313, B:R.313, B:D.341, B:D.343, B:N.347, B:Q.349 Water bridges: B:N.310, B:N.310 pi-Cation interactions: B:R.313, B:R.313

2 x IRF: 1-DEOXY-1-(8-IODO-7-METHYL-2,4-DIOXO-3,4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)-D-RIBITOL(Non-covalent)

IRF.4: 13 residues within 4Å: Chain A: R.9, G.10, V.34, L.35, D.36, N.39, L.40, R.46, F.50, S.96, R.104, L.218, G.342 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.46, A:F.50, A:L.218 Hydrogen bonds: A:G.10, A:V.34, A:D.36, A:N.39, A:S.96, A:S.96, A:R.104, A:R.104 Water bridges: A:R.9, A:G.10, A:V.34 pi-Stacking: A:F.50 IRF.10: 13 residues within 4Å: Chain B: R.9, G.10, V.34, L.35, D.36, N.39, L.40, R.46, F.50, S.96, R.104, L.218, G.342 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:R.46, B:F.50, B:L.218 Hydrogen bonds: B:G.10, B:V.34, B:D.36, B:N.39, B:S.96, B:S.96, B:R.104, B:R.104 Water bridges: B:R.9, B:G.10, B:V.34, B:D.36, B:D.36, B:D.36 pi-Stacking: B:F.50

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 1 residues within 4Å: Chain A: R.167 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.55 Salt bridges: A:R.167 PO4.6: 4 residues within 4Å: Chain A: T.42, R.46, R.336, H.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.42 Salt bridges: A:R.46, A:R.336, A:H.337 PO4.11: 1 residues within 4Å: Chain B: R.167 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.55, B:R.62 Salt bridges: B:R.167 PO4.12: 4 residues within 4Å: Chain B: T.42, R.46, R.336, H.337 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.46, B:R.336, B:H.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klar, T. et al., Natural and Non-Natural Antenna Chromophores in the DNA Photolyase from Thermus Thermophilus. Chembiochem (2006)

Release Date

2007-05-01

Peptides

DEOXYRIBODIPYRIMIDINE PHOTO-LYASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DEOXYRIBODIPYRIMIDINE PHOTO-LYASE

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