SMTL ID : 5o86.1

Mutant of claas II CPD photolyase from Methanosarcina mazei - W388F

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

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

FAD.1: 31 residues within 4Å: Chain A: Y.272, L.284, S.285, N.286, L.287, S.288, L.291, F.318, E.321, I.322, W.325, K.326, S.329, K.392, G.395, R.398, M.399, W.401, A.402, N.423, E.427, D.429, G.430, D.432, N.434, G.435, G.438, I.439, W.441, S.442 Ligands: GOL.12 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:R.398, A:A.402, A:I.439 Hydrogen bonds: A:Y.272, A:S.285, A:S.285, A:N.286, A:L.287, A:S.288, A:S.288, A:S.288, A:E.321, A:R.398, A:R.398, A:R.398, A:N.423, A:D.429, A:D.429, A:N.434, A:N.434, A:G.435 Water bridges: A:G.395, A:G.395, A:G.395, A:Y.436 Salt bridges: A:K.392 pi-Cation interactions: A:R.398

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

SO4.2: 7 residues within 4Å: Chain A: G.85, I.86, R.87, R.235, A.236, F.245, R.425 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.86, A:R.87, A:A.236 Water bridges: A:R.235, A:R.235, A:R.235, A:R.425, A:R.425 Salt bridges: A:R.87, A:R.425 SO4.3: 5 residues within 4Å: Chain A: A.179, A.180, H.181, R.184, W.325 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.181 Water bridges: A:A.180, A:A.180, A:R.184, A:R.184 Salt bridges: A:R.184 SO4.4: 4 residues within 4Å: Chain A: H.176, Y.178, P.346, S.347 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.176 Salt bridges: A:H.176 SO4.5: 5 residues within 4Å: Chain A: Q.97, E.100, T.219, L.220, S.221 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.97, A:E.100, A:L.220, A:S.221, A:S.221, A:S.221 SO4.6: 6 residues within 4Å: Chain A: K.469, F.472, D.473, V.474, K.475, L.476 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.472, A:D.473, A:V.474, A:K.475 Salt bridges: A:K.469 SO4.7: 6 residues within 4Å: Chain A: N.311, P.312, G.313, S.314, K.315, K.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.313, A:K.315, A:K.316 Water bridges: A:S.310 SO4.8: 4 residues within 4Å: Chain A: D.116, G.118, E.119, K.149 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.116, A:G.118, A:E.119 Water bridges: A:K.149, A:K.149 Salt bridges: A:K.149 SO4.9: 3 residues within 4Å: Chain A: S.173, Q.174, K.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.173, A:Q.174 Water bridges: A:K.186 Salt bridges: A:K.186 SO4.10: 6 residues within 4Å: Chain A: S.46, R.47, S.138, L.140, K.143, W.146 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.46, A:S.46, A:S.138 Water bridges: A:R.47, A:R.47, A:S.138

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain A: L.140, R.141, I.142, Y.339, D.340, Y.436 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.142, A:Y.339, A:Y.436, A:Y.436, A:Y.436 GOL.12: 5 residues within 4Å: Chain A: W.325, M.399, G.438, W.441 Ligands: FAD.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ignatz, E. et al., Nicotinamide Adenine Dinucleotides Arrest Photoreduction of Class II DNA Photolyases in FADH ̇ State. Photochem. Photobiol. (2018)

Release Date

2017-09-13

Peptides

Deoxyribodipyrimidine photolyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Deoxyribodipyrimidine photolyase