SMTL ID : 6ptz.1

Crystal structure of pigeon Cryptochrome 4 mutant Y319D in complex with flavin adenine dinucleotide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

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

FAD.1: 29 residues within 4Å: Chain A: T.251, T.252, G.253, L.254, S.255, F.258, S.259, L.289, Q.292, L.293, W.295, R.296, F.299, W.355, H.358, R.361, H.362, A.365, F.384, L.388, D.390, A.391, D.392, I.395, N.396, N.399, W.400, L.403 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:R.361, A:A.365, A:F.384, A:F.384, A:N.399, A:W.400, A:L.403 Hydrogen bonds: A:T.251, A:T.252, A:T.252, A:G.253, A:L.254, A:S.255, A:S.255, A:S.259, A:Q.292, A:H.358, A:R.361, A:D.390, A:D.392, A:N.399, A:N.399 Water bridges: A:S.255, A:S.259, A:H.358 pi-Cation interactions: A:R.361

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.251, L.289, Q.292 Ligands: FAD.1 No protein-ligand interaction detected (PLIP)

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: N.308, Q.311, A.313, G.314 Ligands: PEG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.308 PEG.4: 3 residues within 4Å: Chain A: W.342, T.425, Y.431 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.357, A:A.360 PEG.5: 5 residues within 4Å: Chain A: I.53, R.57, L.61, M.260, L.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.57, A:L.389 Water bridges: A:Y.40 PEG.6: 3 residues within 4Å: Chain A: R.9, K.96, N.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.98 Water bridges: A:Y.37, A:W.97 PEG.7: 5 residues within 4Å: Chain A: A.313, G.314, N.315, Q.320 Ligands: PEG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.314, A:N.315, A:N.315 PEG.8: 2 residues within 4Å: Chain A: I.415, F.416 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.417, A:C.417 PEG.9: 7 residues within 4Å: Chain A: Y.139, L.163, S.164, G.167, F.269, Q.290, L.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.139, A:L.163

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 2 residues within 4Å: Chain A: R.91, E.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.91, A:E.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zoltowski, B.D. et al., Chemical and structural analysis of a photoactive vertebrate cryptochrome from pigeon. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-09-04

Peptides

Cryptochrome-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cryptochrome-1