SMTL ID : 6m79.1

Cryo-EM structure of Arabidopsis CRY under blue light-mediated activation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.1: 5 residues within 4Å: Chain A: N.356, R.357, Y.399, D.406 Ligands: FAD.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.356, A:R.357 Salt bridges: A:R.357 pi-Stacking: A:Y.399 AMP.3: 5 residues within 4Å: Chain B: N.356, R.357, Y.399, D.406 Ligands: FAD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.356, B:R.357, B:Y.399 Salt bridges: B:R.357 pi-Stacking: B:Y.399 AMP.5: 5 residues within 4Å: Chain C: N.356, R.357, Y.399, D.406 Ligands: FAD.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.356, C:R.357 Salt bridges: C:R.357 pi-Stacking: C:Y.399 AMP.7: 5 residues within 4Å: Chain D: N.356, R.357, Y.399, D.406 Ligands: FAD.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.356, D:R.357, D:Y.399 Salt bridges: D:R.357 pi-Stacking: D:Y.399

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

FAD.2: 21 residues within 4Å: Chain A: Y.232, T.244, S.245, L.246, L.247, S.248, L.251, F.287, G.290, I.291, L.293, R.294, W.353, N.356, R.359, D.387, D.389, C.392, D.393, G.396 Ligands: AMP.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.232, A:Y.232, A:T.244, A:S.245, A:L.246, A:L.247, A:S.248, A:S.248, A:N.356, A:R.359, A:R.359, A:R.359, A:D.387, A:D.389 pi-Cation interactions: A:R.359, A:R.359 FAD.4: 21 residues within 4Å: Chain B: Y.232, T.244, S.245, L.246, L.247, S.248, L.251, F.287, G.290, I.291, L.293, R.294, W.353, N.356, R.359, D.387, D.389, C.392, D.393, G.396 Ligands: AMP.3 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Y.232, B:T.244, B:S.245, B:L.246, B:L.247, B:S.248, B:S.248, B:N.356, B:R.359, B:R.359, B:R.359, B:D.387, B:D.389, B:D.393 pi-Cation interactions: B:R.359, B:R.359 FAD.6: 21 residues within 4Å: Chain C: Y.232, T.244, S.245, L.246, L.247, S.248, L.251, F.287, G.290, I.291, L.293, R.294, W.353, N.356, R.359, D.387, D.389, C.392, D.393, G.396 Ligands: AMP.5 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Y.232, C:Y.232, C:T.244, C:S.245, C:L.246, C:L.247, C:S.248, C:S.248, C:N.356, C:R.359, C:R.359, C:R.359, C:D.387, C:D.389 pi-Cation interactions: C:R.359, C:R.359 FAD.8: 21 residues within 4Å: Chain D: Y.232, T.244, S.245, L.246, L.247, S.248, L.251, F.287, G.290, I.291, L.293, R.294, W.353, N.356, R.359, D.387, D.389, C.392, D.393, G.396 Ligands: AMP.7 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Y.232, D:T.244, D:S.245, D:L.246, D:L.247, D:S.248, D:S.248, D:N.356, D:R.359, D:R.359, D:R.359, D:D.387, D:D.389, D:D.393 pi-Cation interactions: D:R.359, D:R.359

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, L. et al., Structural insights into the photoactivation of Arabidopsis CRY2. Nat.Plants (2020)

Release Date

2020-10-14

Peptides

Cryptochrome-2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cryptochrome-2

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