SMTL ID : 1yrx.3 (3 other biounits)

Structure of a novel photoreceptor: the BLUF domain of AppA from Rhodobacter sphaeroides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 16 residues within 4Å: Chain A: Y.9, I.25, T.28, S.29, H.32, N.33, F.49, Q.51, L.53, V.63, H.66, I.67, R.69, D.70, R.72, H.73 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.25, A:F.49, A:R.72 Hydrogen bonds: A:S.29, A:H.32, A:N.33, A:N.33, A:Q.51, A:R.69, A:D.70, A:D.70, A:R.72 Salt bridges: A:H.66 FMN.5: 16 residues within 4Å: Chain B: Y.9, I.25, T.28, S.29, H.32, N.33, F.49, Q.51, L.53, V.63, H.66, I.67, R.69, D.70, R.72, H.73 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.25, B:F.49, B:R.72 Hydrogen bonds: B:S.29, B:N.33, B:N.33, B:Q.51, B:H.66, B:R.69, B:D.70, B:R.72 Salt bridges: B:H.66 FMN.9: 16 residues within 4Å: Chain C: Y.9, I.25, T.28, S.29, H.32, N.33, L.42, F.49, Q.51, V.63, H.66, I.67, D.70, R.72, H.73, W.92 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.25, C:L.42, C:F.49, C:R.72 Hydrogen bonds: C:S.29, C:N.33, C:N.33, C:Q.51, C:D.70, C:D.70, C:R.72 Water bridges: C:R.72 FMN.13: 16 residues within 4Å: Chain D: Y.9, I.25, T.28, S.29, H.32, N.33, L.42, F.49, Q.51, V.63, H.66, I.67, D.70, R.72, H.73, W.92 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.25, D:I.25, D:L.42, D:F.49, D:R.72 Hydrogen bonds: D:H.32, D:N.33, D:N.33, D:Q.51, D:D.70, D:R.72 Salt bridges: D:H.66

9 x D9G: N-DODECYL-N,N-DIMETHYLGLYCINATE(Non-covalent)(Non-functional Binders)

D9G.2: 6 residues within 4Å: Chain A: T.18, L.19, R.20, L.106, L.108 Ligands: D9G.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.108 Hydrogen bonds: A:L.19, A:R.20 D9G.3: 8 residues within 4Å: Chain A: F.43, S.45, Q.46, V.48, F.50 Chain B: F.43, W.52 Ligands: D9G.7 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.43, B:W.52, A:F.43, A:Q.46, A:V.48, A:F.50, A:F.50 D9G.4: 1 residues within 4Å: Ligands: D9G.2 No protein-ligand interaction detected (PLIP) D9G.6: 13 residues within 4Å: Chain B: T.18, L.19, R.20, L.106, L.108 Chain C: L.19, L.23, V.26, E.27, L.96, M.103, L.106 Ligands: D9G.8 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.19, C:L.23, C:V.26, C:L.96, C:L.106, B:L.108 Salt bridges: C:E.27 Hydrogen bonds: B:L.19, B:R.20 D9G.7: 8 residues within 4Å: Chain A: F.43, W.52 Chain B: F.43, S.45, Q.46, V.48, F.50 Ligands: D9G.3 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.43, B:Q.46, B:V.48, B:F.50, B:F.50, A:F.43, A:W.52 D9G.8: 8 residues within 4Å: Chain C: P.15, L.22, Y.44, C.98, D.102, S.105, L.106 Ligands: D9G.6 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.22, C:Y.44, C:D.102, C:L.106, C:L.106 D9G.10: 8 residues within 4Å: Chain A: R.112 Chain B: M.103, E.110, R.112 Chain C: C.98, M.103, E.110 Ligands: D9G.11 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:E.110 Salt bridges: B:R.112, A:R.112 D9G.11: 9 residues within 4Å: Chain B: L.19, L.23, L.96, S.97, D.102, L.106 Chain C: L.19, L.108 Ligands: D9G.10 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.19, B:L.23, B:L.96, B:D.102, B:L.106, C:L.19, C:L.108 D9G.12: 4 residues within 4Å: Chain C: F.43, F.50 Chain D: F.43, F.50 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.43, C:F.50, C:F.50, D:F.43, D:F.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderson, S. et al., Structure of a Novel Photoreceptor, the BLUF Domain of AppA from Rhodobacter sphaeroides. Biochemistry (2005)

Release Date

2005-06-28

Peptides

hypothetical protein Rsph03001874: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
A

D
B

hypothetical protein Rsph03001874

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