- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x CHL: CHLOROPHYLL B(Non-covalent)
- 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 PLIPCL.14: 5 residues within 4Å:- Chain A: Q.37, P.38, L.39, E.40
- Ligands: CD.11
Ligand excluded by PLIPCL.15: 3 residues within 4Å:- Chain A: D.117, K.119
- Ligands: CD.10
Ligand excluded by PLIPCL.31: 3 residues within 4Å:- Chain B: A.1, D.6
- Ligands: CD.26
Ligand excluded by PLIPCL.32: 5 residues within 4Å:- Chain B: Q.37, P.38, L.39, E.40
- Ligands: CD.29
Ligand excluded by PLIPCL.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)
- 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
MB
M
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x CHL: CHLOROPHYLL B(Non-covalent)
- 8 x PID: PERIDININ(Non-covalent)
- 2 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
- 12 x CD: CADMIUM ION(Non-covalent)
- 6 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x K: POTASSIUM ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 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
MB
M