SMTL ID : 2c9e.1

Peridinin-chlorophyll a protein, high-salt form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 20 residues within 4Å: Chain A: W.23, I.29, Y.32, A.66, H.70, L.97, M.100, F.116, L.122, I.203, I.207, I.222, L.226 Ligands: CLA.2, PID.3, PID.4, PID.5, DGD.6, PID.7, DGD.10 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:W.23, A:Y.32, A:A.66, A:F.116, A:F.116, A:I.203, A:I.207, A:I.222, A:L.226 pi-Stacking: A:H.70 Metal complexes: H2O.3 CLA.2: 21 residues within 4Å: Chain A: V.48, L.52, W.197, Y.206, A.240, V.241, H.244, L.271, M.274, F.290, N.293, L.296, Q.297, L.300 Ligands: CLA.1, PID.3, DGD.6, PID.7, PID.8, PID.9, DGD.10 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:V.48, A:L.52, A:W.197, A:Y.206, A:A.240, A:V.241, A:L.271, A:F.290, A:F.290, A:F.290 Hydrogen bonds: A:Q.297 pi-Stacking: A:H.244 Metal complexes: H2O.9

6 x PID: PERIDININ(Non-covalent)

PID.3: 19 residues within 4Å: Chain A: F.21, W.23, I.29, A.30, Q.123, L.126, F.127, N.130, A.135, E.136, Y.139, Y.206, I.207, S.211, M.218 Ligands: CLA.1, CLA.2, PID.5, DGD.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.21, A:W.23, A:I.29, A:I.29, A:I.29, A:A.30, A:L.126, A:F.127, A:F.127, A:F.127, A:A.135, A:Y.139, A:Y.206 Hydrogen bonds: A:Q.123, A:N.130 Water bridges: A:S.211, A:S.211 PID.4: 18 residues within 4Å: Chain A: L.51, G.55, L.56, M.58, M.100, F.109, L.112, R.113, F.142, T.146, Q.234, I.237, N.238 Ligands: CLA.1, PID.5, DGD.6, PID.8, DGD.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.51, A:L.51, A:L.56, A:F.109, A:F.109, A:F.109, A:L.112, A:L.112, A:R.113 Hydrogen bonds: A:Q.234 PID.5: 26 residues within 4Å: Chain A: W.23, H.70, A.73, L.74, A.77, L.83, M.84, A.85, F.90, V.93, N.94, L.97, I.101, K.106, F.109, A.110, F.142, L.145, T.146, V.149, R.150, A.219 Ligands: CLA.1, PID.3, PID.4, DGD.6 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.23, A:W.23, A:A.73, A:A.77, A:L.83, A:A.85, A:F.90, A:V.93, A:L.97, A:K.106, A:F.109, A:F.109, A:F.142, A:L.145, A:T.146, A:V.149 Hydrogen bonds: A:A.85 Water bridges: A:K.106 pi-Stacking: A:F.142 PID.7: 20 residues within 4Å: Chain A: Y.32, I.33, A.36, S.37, A.44, F.116, W.197, S.200, I.203, Q.297, M.298, L.300, F.301, N.304, A.309, Y.313 Ligands: CLA.1, CLA.2, PID.9, DGD.10 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.32, A:A.36, A:F.116, A:W.197, A:W.197, A:I.203, A:I.203, A:I.203, A:L.300, A:L.300, A:L.300, A:F.301, A:A.309, A:Y.313 Hydrogen bonds: A:S.37, A:N.304 Water bridges: A:S.37, A:S.204 PID.8: 19 residues within 4Å: Chain A: V.63, V.67, T.225, A.229, L.230, Q.234, I.237, M.274, F.283, K.284, L.286, L.287, Y.313, F.316 Ligands: CLA.2, PID.4, DGD.6, PID.9, DGD.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.67, A:T.225, A:A.229, A:L.230, A:I.237, A:F.283, A:F.283, A:F.283, A:L.286, A:L.287, A:L.287 Hydrogen bonds: A:Q.234 PID.9: 26 residues within 4Å: Chain A: A.45, M.192, W.197, H.244, A.247, I.248, L.257, V.258, A.259, F.264, V.267, N.268, L.271, I.275, P.280, F.283, K.284, F.316, L.319, T.320, V.323, A.324 Ligands: CLA.2, PID.7, PID.8, DGD.10 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.45, A:W.197, A:W.197, A:A.247, A:F.264, A:V.267, A:L.271, A:F.283, A:F.283, A:K.284, A:L.319, A:V.323 Hydrogen bonds: A:A.259, A:K.284 pi-Stacking: A:F.316

2 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)

DGD.6: 20 residues within 4Å: Chain A: F.10, I.17, A.18, W.23, L.51, F.90, R.113, Q.123, A.135, A.138, Y.139, D.140, F.142, K.143 Ligands: CLA.1, CLA.2, PID.3, PID.4, PID.5, PID.8 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.10, A:I.17, A:I.17, A:A.18, A:W.23, A:W.23, A:L.51, A:F.90, A:A.138, A:F.142 Hydrogen bonds: A:R.113, A:Q.123, A:D.140, A:K.143 Water bridges: A:D.140 DGD.10: 23 residues within 4Å: Chain A: F.184, T.188, I.191, M.192, W.197, F.264, L.286, L.287, F.290, N.293, A.294, Q.297, M.298, A.309, A.312, Y.313, F.316 Ligands: CLA.1, CLA.2, PID.4, PID.7, PID.8, PID.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.184, A:I.191, A:I.191, A:M.192, A:W.197, A:F.264, A:F.290, A:A.312, A:F.316, A:F.316 Hydrogen bonds: A:N.293, A:Y.313, A:Y.313

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 3 residues within 4Å: Chain A: S.71, D.75, D.223 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.71, A:D.75, A:D.223, H2O.4, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulte, T. et al., X-Ray Structure of the High-Salt Form of the Peridinin-Chlorophyll A-Protein from the Dinoflagellate Amphidinium Carterae: Modulation of the Spectral Properties of Pigments by the Protein Environment. Biochemistry (2009)

Release Date

2007-02-20

Peptides

PERIDININ-CHLOROPHYLL A PROTEIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PERIDININ-CHLOROPHYLL A PROTEIN