SMTL ID : 5lfa.1

Crystal structure of iron-sulfur cluster containing bacterial (6-4) photolyase PhrB - Y424F mutant with impaired DNA repair activity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

FAD.1: 27 residues within 4Å: Chain A: F.249, H.265, S.266, L.267, L.268, S.269, N.273, F.303, Q.306, I.307, W.310, R.311, M.314, Y.363, A.364, H.365, H.366, R.369, L.370, Y.391, D.397, A.398, V.402, E.403, N.406, V.407, M.410 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:R.369, A:L.370, A:Y.391, A:Y.391, A:N.406 Hydrogen bonds: A:S.266, A:S.266, A:S.266, A:L.267, A:L.268, A:S.269, A:S.269, A:N.273, A:H.366, A:R.369, A:R.369, A:D.397, A:Y.399, A:N.406, A:N.406 Water bridges: A:H.366 Salt bridges: A:H.265 pi-Cation interactions: A:R.369, A:R.369

1 x DLZ: 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol(Non-covalent)

DLZ.2: 19 residues within 4Å: Chain A: L.8, G.9, D.10, C.32, E.33, V.34, E.37, A.38, Y.40, H.43, I.51, F.52, M.55, F.83, P.104, G.105, E.106, R.108, Y.399 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.51 Hydrogen bonds: A:G.9, A:C.32, A:V.34, A:E.37, A:Y.40, A:G.105, A:R.108

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.3: 8 residues within 4Å: Chain A: C.350, I.431, Y.437, C.438, C.441, Y.443, C.454, F.456 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.350, A:C.438, A:C.441, A:C.454

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: T.346, H.347, Y.443 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.346, A:T.346, A:H.347, A:H.347 GOL.5: 6 residues within 4Å: Chain A: R.56, A.59, E.60, R.63, Y.71, R.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.63, A:R.73 GOL.6: 1 residues within 4Å: Chain A: G.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, F. et al., Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity. Photochem. Photobiol. (2017)

Release Date

2017-01-11

Peptides

(6-4) photolyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

(6-4) photolyase