SMTL ID : 4dja.1

Crystal structure of a prokaryotic (6-4) photolyase PhrB from Agrobacterium Tumefaciens with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore at 1.45A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: F.249, H.265, S.266, L.267, L.268, S.269, I.272, N.273, F.303, Q.306, I.307, W.310, R.311, 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, S.411 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:R.369, A:L.370, A:Y.391, A:Y.391, A:N.406, A:V.407 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:R.311, 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: 18 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, Y.399 7 PLIP interactions: 7 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

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

SF4.3: 11 residues within 4Å: Chain A: M.348, N.349, C.350, G.428, I.431, Y.437, C.438, C.441, Y.443, P.445, C.454 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.350, A:C.438, A:C.441, A:C.454

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: E.103, P.104, D.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.104, A:D.129 Water bridges: A:Q.11

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: P.14, E.65 No protein-ligand interaction detected (PLIP) GOL.6: 3 residues within 4Å: Chain A: F.331, E.332, D.334 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.331, A:D.334, A:D.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, F. et al., Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-04-17

Peptides

Photolyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Photolyase

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