SMTL ID : 2pr5.2 (1 other biounit)

Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark Structure)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.51, A:Q.51, A:Q.51, A:R.64 NA.6: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Q.51, C:Q.51, C:R.64

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain A: V.13, T.15, N.22, N.46, C.47, R.48, L.50, Q.51, V.60, I.63, R.64, L.67, N.79, N.89, L.91, I.93, F.104, V.105, G.106, Q.108 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.15, A:L.67, A:I.93, A:I.93 Hydrogen bonds: A:N.46, A:C.47, A:R.48, A:Q.51, A:N.79, A:N.79, A:N.89, A:Q.108 Water bridges: A:N.22, A:N.46, A:R.48, A:R.48, A:R.64, A:R.64 Salt bridges: A:R.48, A:R.64 FMN.4: 20 residues within 4Å: Chain B: V.13, T.15, N.22, N.46, C.47, R.48, L.50, Q.51, V.60, I.63, R.64, L.67, N.79, N.89, L.91, I.93, F.104, V.105, G.106, Q.108 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.13, B:T.15, B:L.67, B:I.93 Hydrogen bonds: B:N.46, B:C.47, B:R.48, B:Q.51, B:N.79, B:N.79, B:N.89, B:Q.108 Water bridges: B:N.46, B:R.48, B:R.64, B:R.64 Salt bridges: B:R.48, B:R.64 FMN.7: 20 residues within 4Å: Chain C: V.13, T.15, N.22, N.46, C.47, R.48, L.50, Q.51, V.60, I.63, R.64, L.67, N.79, N.89, L.91, I.93, F.104, V.105, G.106, Q.108 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:T.15, C:L.67, C:I.93, C:I.93 Hydrogen bonds: C:N.46, C:C.47, C:R.48, C:Q.51, C:N.79, C:N.79, C:N.89, C:Q.108 Water bridges: C:N.22, C:N.46, C:R.48, C:R.48, C:R.64, C:R.64 Salt bridges: C:R.48, C:R.64 FMN.9: 20 residues within 4Å: Chain D: V.13, T.15, N.22, N.46, C.47, R.48, L.50, Q.51, V.60, I.63, R.64, L.67, N.79, N.89, L.91, I.93, F.104, V.105, G.106, Q.108 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:V.13, D:T.15, D:L.67, D:I.93 Hydrogen bonds: D:N.46, D:C.47, D:R.48, D:Q.51, D:N.79, D:N.79, D:N.89, D:Q.108 Water bridges: D:N.46, D:R.48, D:R.64, D:R.64 Salt bridges: D:R.48, D:R.64

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 4 residues within 4Å: Chain A: R.9, V.10 Chain B: I.107, N.109 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.107, B:N.109 Hydrogen bonds: A:V.10 ACY.5: 3 residues within 4Å: Chain B: H.54, Q.78, M.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.78 Water bridges: B:Q.78 Salt bridges: B:H.54 ACY.8: 4 residues within 4Å: Chain C: R.9, V.10 Chain D: I.107, N.109 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.107, D:N.109 Hydrogen bonds: C:V.10 ACY.10: 3 residues within 4Å: Chain D: H.54, Q.78, M.86 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.78 Water bridges: D:Q.78 Salt bridges: D:H.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moglich, A. et al., Structural Basis for Light-dependent Signaling in the Dimeric LOV Domain of the Photosensor YtvA. J.Mol.Biol. (2007)

Release Date

2007-08-07

Peptides

Blue-light photoreceptor: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Blue-light photoreceptor

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