SMTL ID : 3zq5.1

Structure of the Y263F mutant of the cyanobacterial phytochrome Cph1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 27 residues within 4Å: Chain A: L.15, L.18, I.20, M.174, Y.176, V.186, Y.203, S.206, D.207, I.208, P.209, A.212, F.216, R.222, I.224, R.254, A.256, Y.257, C.259, H.260, F.263, T.274, H.290, A.457, Y.458, L.469, P.471 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.18, A:I.20, A:I.20, A:Y.176, A:V.186, A:Y.203, A:Y.203, A:D.207, A:I.208, A:I.208, A:P.209, A:A.212, A:F.216, A:F.263, A:Y.458, A:L.469 Hydrogen bonds: A:D.207, A:D.207, A:Y.257, A:T.274 Water bridges: A:R.222, A:S.272 Salt bridges: A:R.222, A:R.254, A:H.260 pi-Stacking: A:H.260 CYC.11: 27 residues within 4Å: Chain B: L.15, L.18, I.20, M.174, Y.176, V.186, Y.203, S.206, D.207, I.208, P.209, A.212, F.216, R.222, I.224, R.254, A.256, Y.257, C.259, H.260, F.263, T.274, H.290, A.457, Y.458, L.469, P.471 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:L.18, B:I.20, B:I.20, B:Y.176, B:V.186, B:Y.203, B:Y.203, B:D.207, B:I.208, B:I.208, B:P.209, B:A.212, B:F.216, B:F.263, B:Y.458, B:L.469 Hydrogen bonds: B:D.207, B:D.207, B:Y.257, B:H.260 Water bridges: B:R.222, B:S.272, B:T.274, B:T.274 Salt bridges: B:R.222, B:R.254, B:H.260 pi-Stacking: B:H.260

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: G.200, T.447, N.449 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.200, A:N.449 NA.10: 3 residues within 4Å: Chain A: G.66, F.69, D.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.69, A:D.70 NA.12: 3 residues within 4Å: Chain B: G.200, T.447, N.449 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.200, B:N.449 NA.20: 3 residues within 4Å: Chain B: G.66, F.69, D.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.69

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: R.172, M.195, E.196, Y.198, Q.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.196, A:Y.198, A:Q.292 Salt bridges: A:R.172 PO4.13: 5 residues within 4Å: Chain B: R.172, M.195, E.196, Y.198, Q.292 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.196, B:Q.292 Salt bridges: B:R.172

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

ACT.4: 4 residues within 4Å: Chain A: V.337, K.341, H.355, R.358 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.337 Salt bridges: A:R.358 ACT.5: 6 residues within 4Å: Chain A: E.196, Y.198, Y.203, M.267, G.451, L.477 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.198 Hydrogen bonds: A:Y.203 ACT.6: 2 residues within 4Å: Chain A: R.213, L.283 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.283 Water bridges: A:N.182, A:N.182, A:N.182 Salt bridges: A:R.213 ACT.7: 4 residues within 4Å: Chain A: F.405, S.407, P.488, W.489 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.405 Hydrogen bonds: A:W.489 Water bridges: A:S.407 ACT.14: 4 residues within 4Å: Chain B: V.337, K.341, H.355, R.358 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.337 Salt bridges: B:R.358 ACT.15: 6 residues within 4Å: Chain B: E.196, Y.198, Y.203, M.267, G.451, L.477 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.198 ACT.16: 2 residues within 4Å: Chain B: R.213, L.283 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.283 Water bridges: B:N.182, B:N.182, B:N.182, B:H.282, B:H.282 Salt bridges: B:R.213 ACT.17: 4 residues within 4Å: Chain B: F.405, S.407, P.488, W.489 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.405 Hydrogen bonds: B:W.489 Water bridges: B:S.407

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: E.333, R.358 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.333 GOL.9: 4 residues within 4Å: Chain A: E.162, R.165, R.166, D.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.162 Water bridges: A:R.165 GOL.18: 2 residues within 4Å: Chain B: E.333, R.358 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.333 GOL.19: 4 residues within 4Å: Chain B: E.162, R.165, R.166, D.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.162 Water bridges: B:R.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mailliet, J. et al., Spectroscopy and a High-Resolution Crystal Structure of Tyr263 Mutants of Cyanobacterial Phytochrome Cph1. J.Mol.Biol. (2011)

Release Date

2011-11-30

Peptides

PHYTOCHROME-LIKE PROTEIN CPH1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PHYTOCHROME-LIKE PROTEIN CPH1