SMTL ID : 2x20.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x CHL: CHLOROPHYLL B(Non-covalent)

CHL.1: 18 residues within 4Å: Chain A: F.18, W.24, A.63, A.64, H.67, W.86, L.93, A.133, Y.137, F.140 Chain B: L.42, I.45, I.49 Ligands: PID.2, PID.3, PID.4, PID.5, DGD.6 10 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: A:F.18, A:W.24, A:A.63, A:W.86, A:L.93, A:F.140, B:L.42, B:I.45 pi-Stacking: A:H.67 Metal complexes: H2O.4 CHL.19: 18 residues within 4Å: Chain A: L.42, I.45, I.49 Chain B: F.18, W.24, A.63, A.64, H.67, W.86, L.93, A.133, Y.137, F.140 Ligands: PID.20, PID.21, PID.22, PID.23, DGD.24 10 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:F.18, B:W.24, B:A.63, B:W.86, B:L.93, B:F.140, A:L.42, A:I.45 pi-Stacking: B:H.67 Metal complexes: H2O.12

8 x PID: PERIDININ(Non-covalent)

PID.2: 20 residues within 4Å: Chain A: F.18, V.22, W.24, F.29, L.30, P.121, A.122, M.124, K.125, A.133, Y.137 Chain B: L.36, P.38, A.41, L.42 Ligands: CHL.1, PID.3, PID.5, DGD.6, DGD.24 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:A.41, 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:L.30, A:P.121, A:K.125, A:K.125, A:Y.137 Water bridges: B:Q.37 PID.3: 17 residues within 4Å: Chain A: I.28, F.29, Q.31, A.32, P.33, K.119, V.120, Y.123, M.124 Chain B: I.45, M.48 Ligands: CHL.1, PID.2, DGD.6, PID.21, PID.22, DGD.24 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.28, A:I.28, A:F.29, A:P.33, A:K.119, A:Y.123, A:Y.123 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, K.144 Chain B: L.60, K.61, A.64 Ligands: CHL.1, PID.5, DGD.6, PID.21, PID.22 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.64, A:M.48, A:L.60, A:V.108, A:L.141 pi-Stacking: A:Y.109 PID.5: 27 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, M.106, F.140, F.143, K.144, V.147, K.148, Q.151 Chain B: L.42 Ligands: CHL.1, PID.2, PID.4 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:F.143, A:K.144, A:K.144, A:V.147, A:K.148, A:K.148 Hydrogen bonds: A:T.81, A:E.102 pi-Stacking: A:F.140 PID.20: 20 residues within 4Å: Chain A: L.36, P.38, A.41, L.42 Chain B: F.18, V.22, W.24, F.29, L.30, P.121, A.122, M.124, K.125, A.133, Y.137 Ligands: DGD.6, CHL.19, PID.21, PID.23, DGD.24 15 PLIP interactions: 13 interactions with chain B, 2 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:L.30, B:P.121, B:K.125, B:K.125, B:Y.137, A:A.41 Water bridges: A:Q.37 PID.21: 17 residues within 4Å: Chain A: I.45, M.48 Chain B: I.28, F.29, Q.31, A.32, P.33, K.119, V.120, Y.123, M.124 Ligands: PID.3, PID.4, DGD.6, CHL.19, PID.20, DGD.24 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.28, B:I.28, B:F.29, B:P.33, B:K.119, B:Y.123, B:Y.123 PID.22: 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, K.144 Ligands: PID.3, PID.4, CHL.19, PID.23, DGD.24 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.64, B:M.48, B:L.60, B:V.108, B:L.141 Water bridges: B:Y.109 pi-Stacking: B:Y.109 PID.23: 27 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, M.106, F.140, F.143, K.144, V.147, K.148, Q.151 Ligands: CHL.19, PID.20, PID.22 19 PLIP interactions: 19 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:F.143, B:K.144, B:K.144, 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: 20 residues within 4Å: Chain A: P.33, I.45, M.48, V.108, Y.109, V.112, S.113, T.116, P.121, E.134, Y.137, E.138, L.141 Chain B: L.30 Ligands: CHL.1, PID.2, PID.3, PID.4, PID.20, PID.21 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.30, A:P.33, A:I.45, A:V.108, A:Y.109, A:V.112, A:V.112 Hydrogen bonds: A:Y.109, A:Y.109 Water bridges: A:Y.137 DGD.24: 20 residues within 4Å: Chain A: L.30 Chain B: P.33, I.45, M.48, V.108, Y.109, V.112, S.113, T.116, P.121, E.134, Y.137, E.138, L.141 Ligands: PID.2, PID.3, CHL.19, PID.20, PID.21, PID.22 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.33, B:I.45, B:V.108, B:Y.109, B:V.112, B:V.112, A:L.30 Hydrogen bonds: B:Y.109, B:Y.109, B:E.138 Water bridges: B:Y.137

12 x CD: CADMIUM ION(Non-covalent)

CD.7: 2 residues within 4Å: Chain A: E.3, D.6 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.8: 2 residues within 4Å: Chain A: D.6 Ligands: CL.13 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.6, A:D.6, H2O.1, H2O.1 CD.9: 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.5, H2O.6 CD.10: 2 residues within 4Å: Chain A: D.117 Ligands: CL.15 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.117 CD.11: 3 residues within 4Å: Chain A: E.40 Ligands: CD.12, CL.14 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.40, A:E.40, H2O.3, H2O.3 CD.12: 2 residues within 4Å: Chain A: E.40 Ligands: CD.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.40, H2O.3, H2O.3 CD.25: 2 residues within 4Å: Chain B: E.3, D.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.3, B:D.6, H2O.8, H2O.9 CD.26: 2 residues within 4Å: Chain B: D.6 Ligands: CL.31 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.6, B:D.6, H2O.8, H2O.9 CD.27: 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.13, H2O.13 CD.28: 2 residues within 4Å: Chain B: D.117 Ligands: CL.33 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.117 CD.29: 3 residues within 4Å: Chain B: E.40 Ligands: CD.30, CL.32 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.40, B:E.40, H2O.11, H2O.11 CD.30: 2 residues within 4Å: Chain B: E.40 Ligands: CD.29 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.40, H2O.11, H2O.11

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

CL.13: 3 residues within 4Å: Chain A: A.1, D.6 Ligands: CD.8 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: Q.37, P.38, L.39, E.40 Ligands: CD.11 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: D.117, K.119 Ligands: CD.10 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: A.1, D.6 Ligands: CD.26 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain B: Q.37, P.38, L.39, E.40 Ligands: CD.29 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain B: D.117, K.119 Ligands: CD.28 Ligand excluded by PLIP

2 x K: POTASSIUM ION(Non-covalent)

K.16: 1 residues within 4Å: Chain A: E.134 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.134, H2O.7, H2O.7 K.34: 1 residues within 4Å: Chain B: E.134 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.134, H2O.14, H2O.14

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

NA.17: 2 residues within 4Å: Chain A: D.56, K.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.56, A:K.58 NA.35: 2 residues within 4Å: Chain B: D.56, K.58 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.56, B:K.58

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

PEG.18: 3 residues within 4Å: Chain A: A.1, D.2, R.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.1, A:A.1, A:R.95 Water bridges: A:D.2 PEG.36: 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, B:R.95 Water bridges: B:D.2

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

Related Entries With Identical Sequence