SMTL ID : 5mg0.1

Structure of PAS-GAF fragment of Deinococcus phytochrome by serial femtosecond crystallography

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x LBV: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid(Covalent)

LBV.1: 23 residues within 4Å: Chain A: C.39, E.42, I.44, M.189, Y.191, F.213, F.218, S.221, D.222, I.223, P.224, Y.231, R.269, T.271, S.272, M.274, H.275, Y.278, M.282, S.287, L.288, S.289, H.305 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.44, A:Y.191, A:F.213, A:F.218, A:F.218, A:D.222, A:I.223, A:I.223, A:P.224, A:Y.231 Hydrogen bonds: A:D.222, A:D.222, A:Y.231, A:S.272, A:H.275, A:S.287, A:S.289 Water bridges: A:D.222, A:R.269, A:L.288, A:L.288, A:H.305 Salt bridges: A:R.269, A:H.275 pi-Stacking: A:H.275 LBV.6: 23 residues within 4Å: Chain B: C.39, E.42, I.44, M.189, Y.191, F.213, F.218, S.221, D.222, I.223, P.224, Y.231, R.269, T.271, S.272, M.274, H.275, Y.278, M.282, S.287, L.288, S.289, H.305 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.44, B:Y.191, B:F.213, B:F.218, B:F.218, B:D.222, B:I.223, B:I.223, B:P.224, B:Y.231 Hydrogen bonds: B:D.222, B:D.222, B:Y.231, B:Y.231, B:S.272, B:S.287, B:S.289 Water bridges: B:R.269, B:L.288, B:L.288, B:H.305 Salt bridges: B:R.269, B:H.275 pi-Stacking: B:H.275

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 4 residues within 4Å: Chain A: H.340 Chain B: H.339 Ligands: EDO.5, CL.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.340 NI.7: 4 residues within 4Å: Chain A: H.339 Chain B: H.340 Ligands: CL.3, EDO.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.340

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Ligands: NI.7 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: E.40, P.224, A.225 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Ligands: NI.2 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: E.40, P.224, A.225 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: H.340, H.341 Ligands: NI.2 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain B: H.340, H.341 Ligands: NI.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fuller, F.D. et al., Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat. Methods (2017)

Release Date

2017-02-22

Peptides

Bacteriophytochrome: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bacteriophytochrome

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