SMTL ID : 2x21.1

Structure of Peridinin-Chlorophyll-Protein reconstituted with BChl-a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 17 residues within 4Å: Chain A: F.18, W.24, H.67, W.86, L.93, A.133, A.136, Y.137, F.140 Chain B: L.42, I.49 Ligands: PID.2, PID.3, PID.4, PID.5, DGD.6, PID.30 9 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: A:W.24, A:H.67, A:W.86, A:L.93, A:L.93, A:A.136, A:F.140, B:L.42 Metal complexes: H2O.6 BCL.27: 17 residues within 4Å: Chain A: L.42, I.49 Chain B: F.18, W.24, H.67, W.86, L.93, A.133, A.136, Y.137, F.140 Ligands: PID.4, PID.28, PID.29, PID.30, PID.31, DGD.32 9 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.24, B:H.67, B:W.86, B:L.93, B:L.93, B:A.136, B:F.140, A:L.42 Metal complexes: H2O.15

8 x PID: PERIDININ(Non-covalent)

PID.2: 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: BCL.1, PID.3, PID.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:L.30, A:P.121, A:K.125, A:Y.137 Hydrogen bonds: A:K.125, A:E.134 Water bridges: B:Q.37 PID.3: 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: BCL.1, PID.2, DGD.6, PID.29, PID.30, DGD.32 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.28, A:F.29, A:Y.123, A:Y.123, B:I.45 PID.4: 20 residues within 4Å: Chain A: M.48, I.49, M.51, G.52, L.60, V.105, M.106, V.108, Y.109, F.140, L.141 Chain B: L.60, K.61, A.64 Ligands: BCL.1, PID.5, DGD.6, BCL.27, PID.29, PID.30 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.64, 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 PID.5: 26 residues within 4Å: Chain A: W.24, N.25, 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: BCL.1, PID.2, PID.4 21 PLIP interactions: 21 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:W.86, A:V.89, A:L.93, A:I.97, A:I.97, A:V.105, A:V.105, A:F.140, A:F.143, A:V.147, A:K.148, A:K.148 Hydrogen bonds: A:T.81, A:E.102 pi-Stacking: A:F.140 PID.28: 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: BCL.27, PID.29, PID.31, DGD.32 13 PLIP interactions: 12 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:L.30, B:P.121, B:K.125, B:Y.137 Hydrogen bonds: B:K.125 Water bridges: A:Q.37 PID.29: 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.3, PID.4, DGD.6, BCL.27, PID.28, DGD.32 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.28, B:F.29, B:Y.123, B:Y.123, A:I.45 PID.30: 20 residues within 4Å: Chain A: L.60, K.61, A.64 Chain B: M.48, I.49, M.51, G.52, L.60, V.105, M.106, V.108, Y.109, F.140, L.141 Ligands: BCL.1, PID.3, PID.4, BCL.27, PID.31, DGD.32 11 PLIP interactions: 10 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 Water bridges: B:Y.137 PID.31: 26 residues within 4Å: Chain A: L.42 Chain B: W.24, N.25, 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: BCL.27, PID.28, PID.30 20 PLIP interactions: 20 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:W.86, B:V.89, B:L.93, B:I.97, B:I.97, B:V.105, B:V.105, B:F.140, B:F.143, B:V.147, B:K.148, B:K.148 Hydrogen bonds: B:T.81 pi-Stacking: B:F.140

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

DGD.6: 19 residues within 4Å: Chain A: P.33, I.45, 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: BCL.1, PID.2, PID.3, PID.4, PID.29, DGD.32 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.30, A:P.33, A:I.45, A:Y.109 Hydrogen bonds: A:Y.109, A:Y.109 Water bridges: A:Y.137 DGD.32: 19 residues within 4Å: Chain A: L.30 Chain B: P.33, I.45, M.48, Y.109, V.112, S.113, T.116, P.121, E.134, Y.137, E.138, L.141 Ligands: PID.3, DGD.6, BCL.27, PID.28, PID.29, PID.30 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.33, B:I.45, B:Y.109, A:L.30 Hydrogen bonds: B:Y.109, B:Y.109, B:E.138

14 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.7: 2 residues within 4Å: Chain A: D.6 Ligands: CL.17 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.6, A:D.6, H2O.1 CD.8: 3 residues within 4Å: Chain A: E.3, D.6 Ligands: CL.16 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.3, A:D.6, H2O.1, H2O.2 CD.9: 4 residues within 4Å: Chain A: D.117 Ligands: CD.13, CL.14, CL.18 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.117, H2O.7, H2O.8 CD.10: 2 residues within 4Å: Chain A: N.103, D.107 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.107, A:D.107, H2O.7 CD.11: 2 residues within 4Å: Chain A: E.40 Ligands: CL.15 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.40, A:E.40, H2O.4 CD.12: 1 residues within 4Å: Chain A: E.40 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.40, H2O.4 CD.13: 3 residues within 4Å: Ligands: CD.9, CL.14, CL.18 No protein-ligand interaction detected (PLIP) CD.33: 2 residues within 4Å: Chain B: D.6 Ligands: CL.43 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.6, B:D.6, H2O.10 CD.34: 3 residues within 4Å: Chain B: E.3, D.6 Ligands: CL.42 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.3, B:D.6, H2O.11, H2O.11 CD.35: 4 residues within 4Å: Chain B: D.117 Ligands: CD.39, CL.40, CL.44 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.117, H2O.17, H2O.17 CD.36: 2 residues within 4Å: Chain B: N.103, D.107 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.107, B:D.107, H2O.16 CD.37: 2 residues within 4Å: Chain B: E.40 Ligands: CL.41 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.40, B:E.40, H2O.13 CD.38: 1 residues within 4Å: Chain B: E.40 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.40, H2O.13 CD.39: 3 residues within 4Å: Ligands: CD.35, CL.40, CL.44 No protein-ligand interaction detected (PLIP)

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

CL.14: 4 residues within 4Å: Chain A: K.119 Ligands: CD.9, CD.13, CL.18 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: Q.37, P.38, L.39, E.40 Ligands: CD.11 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: E.3 Ligands: CD.8 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: A.1, D.6 Ligands: CD.7 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: K.35, D.117 Ligands: CD.9, CD.13, CL.14 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: E.134 Ligands: K.24 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: D.56, K.58 Ligands: NA.25 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain B: K.119 Ligands: CD.35, CD.39, CL.44 Ligand excluded by PLIP CL.41: 5 residues within 4Å: Chain B: Q.37, P.38, L.39, E.40 Ligands: CD.37 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain B: E.3 Ligands: CD.34 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain B: A.1, D.6 Ligands: CD.33 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain B: K.35, D.117 Ligands: CD.35, CD.39, CL.40 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain B: E.134 Ligands: K.50 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain B: D.56, K.58 Ligands: NA.51 Ligand excluded by PLIP

8 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.22: 2 residues within 4Å: Chain A: E.102, K.148 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.102, A:E.102 K.23: 2 residues within 4Å: Chain A: K.69, D.85 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.85, H2O.6, H2O.6 K.24: 2 residues within 4Å: Chain A: E.134 Ligands: CL.19 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.134, H2O.8 K.47: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.48: 2 residues within 4Å: Chain B: E.102, K.148 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.102, B:E.102 K.49: 2 residues within 4Å: Chain B: K.69, D.85 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.85, H2O.15, H2O.15 K.50: 2 residues within 4Å: Chain B: E.134 Ligands: CL.45 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.134, H2O.17

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

NA.25: 2 residues within 4Å: Chain A: D.56 Ligands: CL.20 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.58 NA.51: 2 residues within 4Å: Chain B: D.56 Ligands: CL.46 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.58

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

PEG.26: 3 residues within 4Å: Chain A: A.1, D.2, R.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.1, A:A.1 Water bridges: A:D.2, A:R.95, A:R.95 PEG.52: 3 residues within 4Å: Chain B: A.1, D.2, R.95 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.1 Water bridges: B:A.1, B:D.2, B:R.95, B:R.95

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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