SMTL ID : 2x1z.1

Structure of Peridinin-Chlorophyll-Protein reconstituted with Chl-d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

8 x PID: PERIDININ(Non-covalent)

PID.1: 21 residues within 4Å: Chain A: F.18, V.22, W.24, N.26, F.29, L.30, P.121, A.122, M.124, K.125, A.133, E.134, Y.137 Chain B: L.36, P.38, A.41, L.42 Ligands: PID.2, PID.4, CL7.5, DGD.6 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.18, A:V.22, A:W.24, A:F.29, A:F.29, A:F.29, A:F.29, A:F.29, A:P.121, A:K.125, A:K.125, A:Y.137 Hydrogen bonds: A:K.125 Water bridges: B:Q.37 PID.2: 16 residues within 4Å: Chain A: I.28, F.29, Q.31, A.32, P.33, V.120, Y.123, M.124 Chain B: I.45, M.48 Ligands: PID.1, CL7.5, DGD.6, PID.21, PID.22, DGD.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.28, A:I.28, A:F.29, A:Y.123 PID.3: 17 residues within 4Å: Chain A: M.48, I.49, M.51, G.52, L.60, V.105, V.108, Y.109, F.140, L.141 Chain B: L.60, A.64 Ligands: PID.4, CL7.5, DGD.6, PID.21, PID.22 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.48, A:M.51, A:L.60, A:L.60, A:V.108, A:Y.109, A:Y.109, A:Y.109, A:L.141, B:A.64 Water bridges: A:Y.109 PID.4: 25 residues within 4Å: Chain A: W.24, H.67, A.70, I.71, V.74, G.79, V.80, T.81, W.86, V.89, N.90, L.93, I.97, E.102, V.105, F.140, F.143, K.144, V.147, K.148, Q.151 Chain B: L.42 Ligands: PID.1, PID.3, CL7.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.24, A:W.24, A:A.70, A:I.71, A:V.74, A:W.86, A:V.89, A:L.93, A:I.97, A:I.97, A:E.102, A:V.105, A:F.143, A:K.144, A:K.144, A:V.147, A:K.148 Hydrogen bonds: A:T.81 Water bridges: A:E.102 pi-Stacking: A:F.140 PID.20: 21 residues within 4Å: Chain A: L.36, P.38, A.41, L.42 Chain B: F.18, V.22, W.24, N.26, F.29, L.30, P.121, A.122, M.124, K.125, A.133, E.134, Y.137 Ligands: PID.21, PID.23, CL7.24, DGD.25 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.18, B:V.22, B:W.24, B:F.29, B:F.29, B:F.29, B:F.29, B:F.29, B:P.121, B:K.125, B:K.125, B:Y.137 Hydrogen bonds: B:K.125 Water bridges: A:Q.37 PID.21: 16 residues within 4Å: Chain A: I.45, M.48 Chain B: I.28, F.29, Q.31, A.32, P.33, V.120, Y.123, M.124 Ligands: PID.2, PID.3, DGD.6, PID.20, CL7.24, DGD.25 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.28, B:I.28, B:F.29, B:Y.123 PID.22: 17 residues within 4Å: Chain A: L.60, A.64 Chain B: M.48, I.49, M.51, G.52, L.60, V.105, V.108, Y.109, F.140, L.141 Ligands: PID.2, PID.3, PID.23, CL7.24, DGD.25 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.48, B:M.51, B:L.60, B:L.60, B:V.108, B:Y.109, B:Y.109, B:Y.109, B:L.141, A:A.64 PID.23: 25 residues within 4Å: Chain A: L.42 Chain B: W.24, H.67, A.70, I.71, V.74, G.79, V.80, T.81, W.86, V.89, N.90, L.93, I.97, E.102, V.105, F.140, F.143, K.144, V.147, K.148, Q.151 Ligands: PID.20, PID.22, CL7.24 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.24, B:W.24, B:A.70, B:I.71, B:V.74, B:W.86, B:V.89, B:L.93, B:I.97, B:I.97, B:E.102, B:V.105, B:F.143, B:K.144, B:K.144, B:V.147, B:K.148 Hydrogen bonds: B:T.81, B:E.102 Water bridges: B:E.102 pi-Stacking: B:F.140

2 x CL7: CHLOROPHYLL D(Non-covalent)

CL7.5: 19 residues within 4Å: Chain A: F.18, W.24, A.63, A.64, H.67, I.71, W.86, L.93, A.133, A.136, Y.137, F.140 Chain B: I.45, I.49 Ligands: PID.1, PID.2, PID.3, PID.4, DGD.6 11 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.18, A:W.24, A:A.63, A:H.67, A:W.86, A:L.93, A:A.136, A:F.140, B:I.49 pi-Stacking: A:H.67 Metal complexes: H2O.5 CL7.24: 19 residues within 4Å: Chain A: I.45, I.49 Chain B: F.18, W.24, A.63, A.64, H.67, I.71, W.86, L.93, A.133, A.136, Y.137, F.140 Ligands: PID.20, PID.21, PID.22, PID.23, DGD.25 11 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:F.18, B:W.24, B:A.63, B:H.67, B:W.86, B:L.93, B:A.136, B:F.140, A:I.49 pi-Stacking: B:H.67 Metal complexes: H2O.13

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

DGD.6: 17 residues within 4Å: Chain A: P.33, M.48, Y.109, V.112, S.113, T.116, P.121, E.134, Y.137, E.138, L.141 Chain B: L.30 Ligands: PID.1, PID.2, PID.3, CL7.5, PID.21 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.33, A:Y.109, A:Y.109, A:V.112, A:V.112, B:L.30 Hydrogen bonds: A:Y.109, A:Y.109, A:E.138 Water bridges: A:Y.137 DGD.25: 17 residues within 4Å: Chain A: L.30 Chain B: P.33, M.48, Y.109, V.112, S.113, T.116, P.121, E.134, Y.137, E.138, L.141 Ligands: PID.2, PID.20, PID.21, PID.22, CL7.24 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.33, B:Y.109, B:Y.109, B:V.112, B:V.112, A:L.30 Hydrogen bonds: B:Y.109, B:Y.109 Water bridges: B:Y.137, B:Y.137

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain A: A.1, D.6 Ligands: CD.15 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: Q.37, P.38, L.39, E.40 Ligands: CD.18 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: D.56, K.58 Ligands: NA.9 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: D.117, K.119 Ligands: CD.17 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: A.1, D.6 Ligands: CD.34 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain B: Q.37, P.38, L.39, E.40 Ligands: CD.37 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: D.56, K.58 Ligands: NA.28 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain B: D.117, K.119 Ligands: CD.36 Ligand excluded by PLIP

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

NA.9: 3 residues within 4Å: Chain A: D.56, K.58 Ligands: CL.12 No protein-ligand interaction detected (PLIP) NA.10: 3 residues within 4Å: Chain A: K.69, S.73, D.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.69, A:D.85 Water bridges: A:S.82 NA.28: 3 residues within 4Å: Chain B: D.56, K.58 Ligands: CL.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.56 NA.29: 3 residues within 4Å: Chain B: K.69, S.73, D.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.69, B:K.69 Water bridges: B:S.82

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 3 residues within 4Å: Chain A: A.1, D.2, R.95 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.2, A:R.95 PEG.30: 3 residues within 4Å: Chain B: A.1, D.2, R.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.1 Water bridges: B:D.2, B:R.95

12 x CD: CADMIUM ION(Non-covalent)

CD.14: 2 residues within 4Å: Chain A: E.3, D.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.3, A:D.6, H2O.1, H2O.1, H2O.2 CD.15: 2 residues within 4Å: Chain A: D.6 Ligands: CL.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.6, A:D.6, H2O.1 CD.16: 2 residues within 4Å: Chain A: N.103, D.107 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.107, A:D.107, H2O.4, H2O.6 CD.17: 2 residues within 4Å: Chain A: D.117 Ligands: CL.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.117 CD.18: 3 residues within 4Å: Chain A: E.40 Ligands: CL.8, CD.19 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.40, A:E.40, H2O.4 CD.19: 2 residues within 4Å: Chain A: E.40 Ligands: CD.18 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.40, H2O.4, H2O.4 CD.33: 2 residues within 4Å: Chain B: E.3, D.6 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.3, B:D.6, H2O.9, H2O.10, H2O.10 CD.34: 2 residues within 4Å: Chain B: D.6 Ligands: CL.26 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.6, B:D.6, H2O.9 CD.35: 2 residues within 4Å: Chain B: N.103, D.107 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.107, B:D.107, H2O.12, H2O.14 CD.36: 2 residues within 4Å: Chain B: D.117 Ligands: CL.32 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.117 CD.37: 3 residues within 4Å: Chain B: E.40 Ligands: CL.27, CD.38 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.40, B:E.40, H2O.12 CD.38: 2 residues within 4Å: Chain B: E.40 Ligands: CD.37 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.40, H2O.12, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulte, T. et al., X-Ray Structures of the Peridinin-Chlorophyll-Protein Reconstituted with Different Chlorophylls. FEBS Lett. (2010)

Release Date

2010-02-09

Peptides

PERIDININ-CHLOROPHYLL A-BINDING PROTEIN, CHLOROPLASTIC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
M

PERIDININ-CHLOROPHYLL A-BINDING PROTEIN, CHLOROPLASTIC

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