SMTL ID : 5k5b.1

Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 1 residues within 4Å: Chain A: I.201 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.201 ACT.2: 3 residues within 4Å: Chain A: T.197, R.216, F.217 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.197, A:R.216 ACT.3: 4 residues within 4Å: Chain A: R.186, L.209, V.283, H.304 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.283, A:H.304 Salt bridges: A:R.186, A:H.210, A:H.304 ACT.6: 1 residues within 4Å: Chain B: I.201 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.201 ACT.7: 3 residues within 4Å: Chain B: T.197, R.216, F.217 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.197, B:R.216 ACT.8: 4 residues within 4Å: Chain B: R.186, L.209, V.283, H.304 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.283, B:H.304 Salt bridges: B:R.186, B:H.210, B:H.304

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 7 residues within 4Å: Chain A: P.272, M.273, Q.276 Chain B: P.272, M.273, Q.276 Ligands: MPD.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.272 Hydrogen bonds: B:Q.276, A:Q.276 Water bridges: B:E.32 MPD.9: 7 residues within 4Å: Chain A: P.272, M.273, Q.276 Chain B: P.272, M.273, Q.276 Ligands: MPD.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.272 Hydrogen bonds: A:Q.276, B:Q.276 Water bridges: B:E.32

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.5: 27 residues within 4Å: Chain A: T.34, T.35, C.38, E.41, I.43, M.188, Y.190, F.212, F.217, S.220, D.221, I.222, P.223, A.226, Y.230, R.236, R.268, T.270, S.271, M.273, H.274, Y.277, S.286, L.287, S.288, L.300, H.304 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.43, A:I.43, A:Y.190, A:F.212, A:F.217, A:F.217, A:D.221, A:I.222, A:I.222, A:P.223, A:A.226, A:Y.230, A:M.273, A:H.274, A:Y.277, A:L.300 Hydrogen bonds: A:D.221, A:D.221, A:D.221, A:Y.230, A:S.271, A:S.286 Water bridges: A:R.268, A:R.268, A:L.287, A:L.287, A:H.304 Salt bridges: A:R.268, A:H.274 pi-Stacking: A:H.274 LBV.10: 27 residues within 4Å: Chain B: T.34, T.35, C.38, E.41, I.43, M.188, Y.190, F.212, F.217, S.220, D.221, I.222, P.223, A.226, Y.230, R.236, R.268, T.270, S.271, M.273, H.274, Y.277, S.286, L.287, S.288, L.300, H.304 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:I.43, B:I.43, B:Y.190, B:F.212, B:F.217, B:F.217, B:D.221, B:I.222, B:I.222, B:P.223, B:A.226, B:Y.230, B:M.273, B:H.274, B:Y.277, B:L.300 Hydrogen bonds: B:D.221, B:D.221, B:Y.230, B:Y.230, B:S.271, B:S.286 Water bridges: B:R.268, B:R.268, B:H.274, B:H.274, B:L.287, B:L.287, B:H.304 Salt bridges: B:R.268, B:H.274 pi-Stacking: B:H.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edlund, P. et al., The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography. Sci Rep (2016)

Release Date

2016-10-26

Peptides

Bacteriophytochrome: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bacteriophytochrome

Related Entries With Identical Sequence