SMTL ID : 4our.1

Crystal structure of Arabidopsis thaliana phytochrome B photosensory module

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-1-mer

Ligands

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: K.148, R.152 Chain B: R.94 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.94 Salt bridges: A:K.148, A:R.152 SO4.2: 4 residues within 4Å: Chain A: Q.489, R.490, M.491, H.492 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.491, A:H.492, A:H.492 Salt bridges: A:H.492 SO4.3: 3 residues within 4Å: Chain A: R.177, R.204, D.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.205 Salt bridges: A:R.177 SO4.4: 3 residues within 4Å: Chain A: T.80, S.81, K.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.81 Salt bridges: A:K.107 SO4.5: 1 residues within 4Å: Chain A: R.76 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.76 SO4.6: 3 residues within 4Å: Chain A: Q.21, R.22, Q.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.254 Salt bridges: A:R.22 SO4.7: 3 residues within 4Å: Chain A: K.229, R.307, L.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.308 Salt bridges: A:K.229, A:R.307 SO4.11: 3 residues within 4Å: Chain B: R.490, R.494 Ligands: O6E.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.218 Salt bridges: B:R.490 SO4.12: 2 residues within 4Å: Chain B: R.19, G.488 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.488 Salt bridges: B:R.19 SO4.13: 3 residues within 4Å: Chain B: R.177, R.204, D.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.205 Salt bridges: B:R.177 SO4.14: 2 residues within 4Å: Chain B: T.80, S.81 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.81

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: R.184, L.207, E.208, Y.210, M.277, G.278, S.279, H.315 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.184, A:E.208, A:Y.210, A:Y.210 GOL.10: 5 residues within 4Å: Chain A: I.154, Q.158, F.332 Chain B: F.332, Q.335 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.158, B:F.332

2 x O6E: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid(Covalent)

O6E.9: 27 residues within 4Å: Chain A: Y.16, I.20, M.186, Y.188, V.198, Y.215, T.218, D.219, I.220, P.221, S.224, F.228, R.234, I.236, R.264, P.266, H.267, C.269, H.270, Y.273, M.277, S.282, A.284, V.313, H.315, R.490, H.492 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.16, A:I.20, A:Y.188, A:V.198, A:Y.215, A:Y.215, A:I.220, A:I.220, A:P.221, A:F.228, A:Y.273, A:A.284, A:V.313, A:R.490 Hydrogen bonds: A:D.219, A:D.219, A:H.267, A:S.282 Water bridges: A:H.315 Salt bridges: A:R.234, A:R.234, A:R.264, A:H.270 pi-Stacking: A:Y.188 pi-Cation interactions: A:H.270 O6E.16: 27 residues within 4Å: Chain B: Y.16, I.20, M.186, Y.188, Y.215, T.218, D.219, I.220, P.221, S.224, F.228, R.234, I.236, R.264, P.266, H.267, C.269, H.270, Y.273, M.277, A.284, L.311, V.313, H.315, R.490, H.492 Ligands: SO4.11 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:Y.16, B:I.20, B:Y.188, B:Y.215, B:Y.215, B:D.219, B:I.220, B:I.220, B:F.228, B:H.267, B:H.270, B:A.284, B:L.311, B:V.313, B:R.490 Hydrogen bonds: B:D.219, B:D.219, B:D.219, B:H.267, B:H.270 Water bridges: B:H.270 Salt bridges: B:R.234, B:R.234, B:R.264, B:H.270 pi-Cation interactions: B:H.270

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.15: 5 residues within 4Å: Chain B: W.103, Y.114, E.134, G.142, Q.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.114, B:Q.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgie, E.S. et al., Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-07-16

Peptides

Phytochrome B: A
Phytochrome B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phytochrome B

Phytochrome B