SMTL ID : 1u3d.1

Crystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana with AMPPNP bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Ligands: ANP.7 No protein-ligand interaction detected (PLIP) MG.2: 7 residues within 4Å: Chain A: N.238, R.239, K.241, T.246, T.247, H.358 Ligands: MG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.238, A:T.246 MG.3: 5 residues within 4Å: Chain A: K.241, S.244, T.246, H.358 Ligands: MG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.244, A:T.246 MG.4: 4 residues within 4Å: Chain A: N.219, K.222, A.223 Ligands: NDS.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.219

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

CL.5: 1 residues within 4Å: Chain A: H.318 Ligand excluded by PLIP

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

FAD.6: 28 residues within 4Å: Chain A: Y.235, T.247, S.248, F.249, L.250, S.251, L.254, F.290, S.293, I.294, L.296, R.297, W.356, L.357, D.359, R.362, V.363, S.366, F.384, L.388, D.390, A.391, D.392, S.395, D.396, G.399, W.400 Ligands: ANP.7 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:R.362, A:V.363, A:F.384 Hydrogen bonds: A:S.248, A:F.249, A:L.250, A:S.251, A:S.251, A:S.293, A:D.359, A:D.359, A:D.359, A:R.362, A:R.362, A:D.390, A:D.392, A:S.395 Water bridges: A:D.359, A:S.395 pi-Cation interactions: A:R.362, A:R.362

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.7: 13 residues within 4Å: Chain A: F.158, R.239, R.240, K.292, L.296, D.359, R.360, V.363, L.398, Y.402, D.409 Ligands: MG.1, FAD.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.239, A:R.240, A:R.360, A:R.360, A:D.409 Salt bridges: A:K.292 pi-Stacking: A:Y.402, A:Y.402

1 x NDS: ETHYL DIMETHYL AMMONIO PROPANE SULFONATE(Non-covalent)

NDS.8: 8 residues within 4Å: Chain A: A.212, W.213, S.214, N.219, A.223, F.249, H.253 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.249 Hydrogen bonds: A:S.214, A:S.214 Salt bridges: A:K.222, A:H.253 pi-Cation interactions: A:W.213, A:F.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brautigam, C.A. et al., Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-08-24

Peptides

Cryptochrome 1 apoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cryptochrome 1 apoprotein

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