SMTL ID : 7qd0.1

Structure of the orange carotenoid protein from Planktothrix agardhii binding echinenone in the C2 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x ARG: ARGININE(Non-covalent)

ARG.1: 2 residues within 4Å: Chain A: N.14, V.318 2 PLIP interactions: 2 interactions with chain A, Hydrogen bonds: A:V.318 Salt bridges: A:E.260 ARG.10: 2 residues within 4Å: Chain B: N.14, V.318 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.318 Salt bridges: B:E.260

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: R.155, P.227, P.228, Q.230, F.242, E.246 Ligands: ECH.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.155, A:Q.230 Water bridges: A:R.155, A:N.156 GOL.4: 4 residues within 4Å: Chain A: R.187, N.202, N.205, N.206 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.187, A:N.202, A:N.206 Water bridges: A:T.188, A:N.202, A:N.205, A:N.205 GOL.7: 1 residues within 4Å: Chain B: A.282 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.276 GOL.8: 1 residues within 4Å: Chain A: N.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.32, A:N.32 Water bridges: A:S.132 GOL.9: 2 residues within 4Å: Chain A: Q.62, F.63 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.62 GOL.11: 7 residues within 4Å: Chain B: R.155, P.227, P.228, Q.230, F.242, E.246 Ligands: ECH.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.155, B:Q.230 Water bridges: B:R.155, B:N.156 GOL.13: 4 residues within 4Å: Chain B: R.187, N.202, N.205, N.206 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.187, B:N.202, B:N.206 Water bridges: B:T.188, B:N.202, B:N.205, B:N.205 GOL.16: 1 residues within 4Å: Chain A: A.282 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.276 GOL.17: 1 residues within 4Å: Chain B: N.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.32, B:N.32 Water bridges: B:S.132 GOL.18: 2 residues within 4Å: Chain B: Q.62, F.63 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.62

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

ACT.3: 6 residues within 4Å: Chain A: T.17, Q.226, P.227, P.228, F.229, D.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.226, A:F.229 Water bridges: A:R.9 ACT.5: 7 residues within 4Å: Chain A: K.49, E.115, Q.119 Chain B: F.280, G.281, A.282, G.283 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.282, A:Q.119 Hydrogen bonds: B:A.282, B:G.283 Salt bridges: A:K.49 ACT.12: 6 residues within 4Å: Chain B: T.17, Q.226, P.227, P.228, F.229, D.306 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.226, B:F.229, B:D.306 Water bridges: B:R.9 ACT.14: 7 residues within 4Å: Chain A: F.280, G.281, A.282, G.283 Chain B: K.49, E.115, Q.119 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.282, B:Q.119 Hydrogen bonds: A:A.282, A:G.283 Salt bridges: B:K.49

2 x ECH: beta,beta-caroten-4-one(Non-covalent)

ECH.6: 28 residues within 4Å: Chain A: L.37, I.40, W.41, Y.44, L.107, W.110, Y.111, G.114, M.117, I.151, T.152, R.155, V.158, Y.203, M.207, F.242, C.247, L.250, L.252, V.275, T.277, W.279, F.280, M.286, M.288, W.290, I.305 Ligands: GOL.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.37, A:I.40, A:W.41, A:Y.44, A:L.107, A:W.110, A:W.110, A:W.110, A:W.110, A:I.151, A:R.155, A:V.158, A:F.242, A:F.242, A:L.250, A:L.252, A:V.275, A:W.279, A:W.279, A:F.280, A:W.290, A:I.305, A:I.305 ECH.15: 28 residues within 4Å: Chain B: L.37, I.40, W.41, Y.44, L.107, W.110, Y.111, G.114, M.117, I.151, T.152, R.155, V.158, Y.203, M.207, F.242, C.247, L.250, L.252, V.275, T.277, W.279, F.280, M.286, M.288, W.290, I.305 Ligands: GOL.11 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.37, B:I.40, B:W.41, B:Y.44, B:L.107, B:W.110, B:W.110, B:W.110, B:W.110, B:I.151, B:R.155, B:V.158, B:F.242, B:F.242, B:L.250, B:L.252, B:V.275, B:W.279, B:W.279, B:F.280, B:W.290, B:I.305, B:I.305 Hydrogen bonds: B:Y.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilson, A. et al., Structure-function-dynamics relationships in the peculiar Planktothrix PCC7805 OCP1: Impact of his-tagging and carotenoid type. Biochim Biophys Acta Bioenerg (2022)

Release Date

2022-07-06

Peptides

Orange carotenoid-binding protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Orange carotenoid-binding protein

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