SMTL ID : 3iiu.1

Structure of the reconstituted Peridinin-Chlorophyll a-Protein (RFPCP) mutant N89L

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 20 residues within 4Å: Chain A: L.11, F.18, W.24, A.63, A.64, H.67, I.71, L.90, L.93, A.133, A.136, Y.137, F.140 Chain B: I.49 Ligands: PID.2, PID.3, PID.4, PID.5, J7Z.6, PID.19 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.11, A:W.24, A:A.63, A:H.67, A:I.71, A:L.90, A:L.93, A:A.136, A:F.140 pi-Stacking: A:H.67 Metal complexes: H2O.7 CLA.16: 20 residues within 4Å: Chain A: I.49 Chain B: L.11, F.18, W.24, A.63, A.64, H.67, I.71, L.90, L.93, A.133, A.136, Y.137, F.140 Ligands: PID.4, PID.17, PID.18, PID.19, PID.20, J7Z.21 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:L.11, B:W.24, B:A.63, B:H.67, B:I.71, B:L.90, B:L.93, B:A.136, B:F.140 pi-Stacking: B:H.67 Metal complexes: H2O.18

8 x PID: PERIDININ(Non-covalent)

PID.2: 21 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, E.134, Y.137 Chain B: L.36, P.38, A.41, L.42 Ligands: CLA.1, PID.3, PID.5, J7Z.6, J7Z.21 15 PLIP interactions: 14 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:L.30, A:P.121, A:K.125, A:K.125, A:Y.137 Hydrogen bonds: A:K.125 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: CLA.1, PID.2, J7Z.6, PID.18, PID.19, J7Z.21 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.28, A:I.28, A:F.29, A:K.119, A:V.120, A:Y.123, B:I.45 PID.4: 20 residues within 4Å: Chain A: M.48, I.49, M.51, G.52, V.105, M.106, V.108, Y.109, Y.137, F.140, L.141 Chain B: L.60, K.61, A.64 Ligands: CLA.1, PID.5, J7Z.6, CLA.16, PID.18, PID.19 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.51, A:V.108, A:L.141, B:A.64 Water bridges: A:Y.109 pi-Stacking: A:Y.109 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, L.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: CLA.1, PID.2, PID.4 18 PLIP interactions: 18 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.90, A:L.93, A:I.97, A:I.97, A:F.140, A:F.140, A:F.143, A:V.147, A:K.148 Hydrogen bonds: A:T.81 Water bridges: A:K.148 PID.17: 21 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, E.134, Y.137 Ligands: J7Z.6, CLA.16, PID.18, PID.20, J7Z.21 15 PLIP interactions: 1 interactions with chain A, 14 interactions with chain B Water bridges: A:Q.37 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 Hydrogen bonds: B:K.125 PID.18: 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, J7Z.6, CLA.16, PID.17, J7Z.21 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.28, B:I.28, B:F.29, B:K.119, B:V.120, B:Y.123, A:I.45 PID.19: 20 residues within 4Å: Chain A: L.60, K.61, A.64 Chain B: M.48, I.49, M.51, G.52, V.105, M.106, V.108, Y.109, Y.137, F.140, L.141 Ligands: CLA.1, PID.3, PID.4, CLA.16, PID.20, J7Z.21 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.51, B:V.108, B:L.141, A:A.64 pi-Stacking: B:Y.109 PID.20: 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, L.90, L.93, I.97, E.102, V.105, F.140, F.143, K.144, V.147, K.148, Q.151 Ligands: CLA.16, PID.17, PID.19 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.90, B:L.93, B:I.97, B:I.97, B:F.140, B:F.140, B:F.143, B:V.147, B:K.148 Hydrogen bonds: B:T.81, B:E.102 Water bridges: B:K.148

2 x J7Z: (2S)-3-[(6-O-alpha-D-galactopyranosyl-beta-D-galactopyranosyl)oxy]-2-[(3Z,6Z,9Z,12Z,15Z)-octadeca-3,6,9,12,15-pentaenoyloxy]propyl (5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoate(Non-covalent)

J7Z.6: 22 residues within 4Å: Chain A: P.33, I.45, M.48, V.108, Y.109, V.112, S.113, T.116, V.120, P.121, E.134, Y.137, E.138, L.141 Chain B: L.30 Ligands: CLA.1, PID.2, PID.3, PID.4, PID.17, PID.18, J7Z.21 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.33, A:P.33, A:I.45, A:V.108, A:Y.109, A:Y.109, A:V.112, A:V.120, B:L.30 Hydrogen bonds: A:Y.109, A:Y.109, A:E.134, A:E.134, A:E.138 Water bridges: A:Y.137 J7Z.21: 22 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, V.120, P.121, E.134, Y.137, E.138, L.141 Ligands: PID.2, PID.3, J7Z.6, CLA.16, PID.17, PID.18, PID.19 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.33, B:P.33, B:I.45, B:V.108, B:Y.109, B:Y.109, B:V.112, B:V.120, A:L.30 Hydrogen bonds: B:Y.109, B:E.134 Water bridges: B:Y.137

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

CD.7: 3 residues within 4Å: Chain A: E.3, D.6 Ligands: CL.12 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.3, A:D.6, H2O.3, H2O.3, H2O.3 CD.8: 2 residues within 4Å: Chain A: D.6 Ligands: CL.15 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.6, A:D.6, H2O.3, H2O.6 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.4, H2O.8 CD.10: 4 residues within 4Å: Chain A: D.117 Ligands: CD.11, CL.13, CL.14 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.117, H2O.3, H2O.6 CD.11: 3 residues within 4Å: Ligands: CD.10, CL.13, CL.14 No protein-ligand interaction detected (PLIP) CD.22: 3 residues within 4Å: Chain B: E.3, D.6 Ligands: CL.27 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.3, B:D.6, H2O.14, H2O.14, H2O.14 CD.23: 2 residues within 4Å: Chain B: D.6 Ligands: CL.30 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.6, B:D.6, H2O.14, H2O.17 CD.24: 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.15, H2O.19 CD.25: 4 residues within 4Å: Chain B: D.117 Ligands: CD.26, CL.28, CL.29 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.117, H2O.14, H2O.17 CD.26: 3 residues within 4Å: Ligands: CD.25, CL.28, CL.29 No protein-ligand interaction detected (PLIP)

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

CL.12: 2 residues within 4Å: Chain A: E.3 Ligands: CD.7 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: K.35, D.117 Ligands: CD.10, CD.11, CL.14 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: K.119 Ligands: CD.10, CD.11, CL.13 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: A.1, D.6 Ligands: CD.8 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: E.3 Ligands: CD.22 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain B: K.35, D.117 Ligands: CD.25, CD.26, CL.29 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain B: K.119 Ligands: CD.25, CD.26, CL.28 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: A.1, D.6 Ligands: CD.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulte, T. et al., Identification of a single peridinin sensing Chl-a excitation in reconstituted PCP by crystallography and spectroscopy. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-11-24

Peptides

Peridinin-chlorophyll a-binding protein 1, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
M

Peridinin-chlorophyll a-binding protein 1, chloroplastic