SMTL ID : 1yrx.4 (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-hexamer

Ligands

6 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, 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 A Hydrophobic interactions: A:I.25, A:L.42, A:F.49, A:R.72 Hydrogen bonds: A:S.29, A:N.33, A:N.33, A:Q.51, A:D.70, A:D.70, A:R.72 Water bridges: A:R.72 FMN.5: 16 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:I.25, B:I.25, B:L.42, B:F.49, B:R.72 Hydrogen bonds: B:H.32, B:N.33, B:N.33, B:Q.51, B:D.70, B:R.72 Salt bridges: B:H.66 FMN.6: 16 residues within 4Å: Chain C: 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 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.25, C:F.49, C:R.72 Hydrogen bonds: C:S.29, C:H.32, C:N.33, C:N.33, C:Q.51, C:R.69, C:D.70, C:D.70, C:R.72, A:A.1 Salt bridges: C:H.66 FMN.10: 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:L.42, D:F.49, D:R.72 Hydrogen bonds: D:S.29, D:H.32, D:N.33, D:N.33, D:Q.51, D:D.70, D:R.72 Water bridges: D:R.72 FMN.14: 16 residues within 4Å: Chain E: 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 E Hydrophobic interactions: E:I.25, E:I.25, E:L.42, E:F.49, E:R.72 Hydrogen bonds: E:N.33, E:N.33, E:Q.51, E:D.70, E:D.70, E:R.72 Salt bridges: E:H.66 FMN.15: 16 residues within 4Å: Chain F: 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: 12 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:I.25, F:F.49, F:R.72 Hydrogen bonds: F:S.29, F:N.33, F:N.33, F:Q.51, F:H.66, F:R.69, F:D.70, F:R.72, D:A.1 Salt bridges: F:H.66

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

D9G.2: 8 residues within 4Å: Chain A: C.98, M.103, E.110 Chain D: I.114 Chain E: E.110, S.111, R.112 Ligands: D9G.3 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: A:E.110, D:I.114, E:R.112 Salt bridges: E:R.112 D9G.3: 4 residues within 4Å: Chain A: L.19, L.108 Chain D: I.114 Ligands: D9G.2 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.19, A:L.108, D:I.114, D:I.114 D9G.4: 4 residues within 4Å: Chain A: F.43, F.50 Chain B: F.43, F.50 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.43, A:F.50, A:F.50, B:F.43, B:F.50 D9G.7: 6 residues within 4Å: Chain C: T.18, L.19, R.20, L.106, L.108 Ligands: D9G.9 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.108 Hydrogen bonds: C:L.19, C:R.20 D9G.8: 5 residues within 4Å: Chain C: F.43, S.45, Q.46, V.48, F.50 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.43, C:Q.46, C:V.48, C:F.50, C:F.50 D9G.9: 1 residues within 4Å: Ligands: D9G.7 No protein-ligand interaction detected (PLIP) D9G.11: 8 residues within 4Å: Chain A: I.114 Chain B: E.110, S.111, R.112 Chain D: C.98, M.103, E.110 Ligands: D9G.12 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:I.114, B:R.112, D:E.110 Salt bridges: B:R.112 D9G.12: 4 residues within 4Å: Chain A: I.114 Chain D: L.19, L.108 Ligands: D9G.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.114, A:I.114, D:L.19, D:L.108 D9G.13: 4 residues within 4Å: Chain D: F.43, F.50 Chain E: F.43, F.50 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:F.43, D:F.50, D:F.50, E:F.43, E:F.50 D9G.16: 6 residues within 4Å: Chain F: T.18, L.19, R.20, L.106, L.108 Ligands: D9G.18 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.108 Hydrogen bonds: F:L.19, F:R.20 D9G.17: 5 residues within 4Å: Chain F: F.43, S.45, Q.46, V.48, F.50 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.43, F:Q.46, F:V.48, F:F.50, F:F.50 D9G.18: 1 residues within 4Å: Ligands: D9G.16 No protein-ligand interaction detected (PLIP)

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

hypothetical protein Rsph03001874

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