SMTL ID : 1ppr.1

PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

6 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 15 residues within 4Å: Chain A: F.17, A.62, A.63, H.66, W.85, L.92, A.132, Y.136, F.139, I.211 Ligands: PID.3, PID.4, PID.5, PID.6, DGD.11 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.17, A:F.17, A:A.62, A:W.85, A:L.92, A:F.139 pi-Stacking: A:H.66 Metal complexes: H2O.75 CLA.2: 19 residues within 4Å: Chain A: I.44, I.48, F.180, L.181, I.184, W.186, A.225, A.226, H.229, Y.247, L.254, Y.270, A.297, F.301 Ligands: PID.7, PID.8, PID.9, PID.10, DGD.12 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.44, A:F.180, A:F.180, A:L.181, A:I.184, A:W.186, A:A.225, A:L.254, A:Y.270, A:A.297, A:F.301, A:F.301 pi-Stacking: A:H.229 Metal complexes: H2O.52 CLA.13: 15 residues within 4Å: Chain B: F.17, A.62, A.63, H.66, W.85, L.92, A.132, Y.136, F.139, I.211 Ligands: PID.15, PID.16, PID.17, PID.18, DGD.23 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.17, B:F.17, B:A.62, B:H.66, B:W.85, B:L.92, B:F.139 pi-Stacking: B:H.66 Metal complexes: H2O.213 CLA.14: 18 residues within 4Å: Chain B: I.44, I.48, F.180, I.184, W.186, A.225, A.226, H.229, Y.247, L.254, Y.270, A.297, F.301 Ligands: PID.19, PID.20, PID.21, PID.22, DGD.24 12 PLIP interactions: 11 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.44, B:F.180, B:F.180, B:I.184, B:W.186, B:A.225, B:L.254, B:Y.270, B:F.301, B:F.301 pi-Stacking: B:H.229 Metal complexes: H2O.191 CLA.25: 15 residues within 4Å: Chain C: F.17, A.62, A.63, H.66, W.85, L.92, A.132, Y.136, F.139, I.211 Ligands: PID.27, PID.28, PID.29, PID.30, DGD.35 8 PLIP interactions: 7 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:F.17, C:F.17, C:A.62, C:W.85, C:L.92, C:F.139 pi-Stacking: C:H.66 Metal complexes: H2O.359 CLA.26: 18 residues within 4Å: Chain C: I.44, I.48, F.180, I.184, W.186, A.225, A.226, H.229, Y.247, L.254, Y.270, A.297, F.301 Ligands: PID.31, PID.32, PID.33, PID.34, DGD.36 11 PLIP interactions: 10 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:I.44, C:F.180, C:F.180, C:I.184, C:W.186, C:A.225, C:Y.270, C:F.301, C:F.301 pi-Stacking: C:H.229 Metal complexes: H2O.336

24 x PID: PERIDININ(Non-covalent)

PID.3: 21 residues within 4Å: Chain A: F.17, V.21, W.23, N.25, F.28, L.29, P.120, A.121, M.123, K.124, A.132, E.133, Y.136, A.200, S.203, I.207 Ligands: CLA.1, PID.4, PID.6, DGD.11, DGD.12 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.17, A:V.21, A:W.23, A:F.28, A:F.28, A:F.28, A:F.28, A:P.120, A:M.123, A:K.124, A:K.124, A:Y.136, A:I.207 Hydrogen bonds: A:K.124, A:S.203 PID.4: 20 residues within 4Å: Chain A: I.27, F.28, Q.30, A.31, P.32, D.116, K.118, V.119, Y.122, M.123, I.207, M.210 Chain B: L.292, A.296 Ligands: CLA.1, PID.3, PID.8, PID.9, DGD.11, DGD.12 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.27, A:I.27, A:F.28, A:P.32, A:K.118, A:V.119, A:Y.122, A:Y.122, B:A.296 PID.5: 19 residues within 4Å: Chain A: M.47, I.48, M.50, G.51, V.104, M.105, V.107, Y.108, Y.136, L.140, K.143, L.222, K.223, A.226 Ligands: CLA.1, PID.6, PID.8, PID.9, DGD.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:M.47, A:V.107, A:Y.108, A:Y.108, A:Y.108, A:L.140, A:A.226 PID.6: 26 residues within 4Å: Chain A: W.23, N.24, H.66, A.69, I.70, I.73, G.78, V.79, T.80, W.85, V.88, N.89, L.92, I.96, E.101, V.104, F.139, F.142, K.143, V.146, Q.150, Q.201, L.204 Ligands: CLA.1, PID.3, PID.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.23, A:W.23, A:I.70, A:I.73, A:W.85, A:V.88, A:L.92, A:I.96, A:V.104, A:F.139, A:F.142, A:K.143, A:K.143 Hydrogen bonds: A:T.80, A:K.147, A:Q.201 PID.7: 20 residues within 4Å: Chain A: A.31, L.35, P.37, A.40, F.180, I.184, W.186, Y.191, M.192, P.282, L.283, M.285, F.286, A.294, A.298 Ligands: CLA.2, PID.8, PID.10, DGD.11, DGD.12 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.184, A:Y.191, A:Y.191, A:Y.191, A:P.282, A:M.285, A:F.286, A:F.286 Water bridges: C:V.198 PID.8: 17 residues within 4Å: Chain A: I.44, M.47, V.190, Y.191, K.193, P.196, I.281, N.284, M.285 Chain B: S.280, L.283 Ligands: CLA.2, PID.4, PID.5, PID.7, DGD.11, DGD.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.196, A:I.281 Hydrogen bonds: A:N.284 PID.9: 17 residues within 4Å: Chain A: L.59, K.60, A.63, M.210, I.211, M.213, G.214, V.266, M.267, V.269, Y.270, Y.302 Ligands: CLA.2, PID.4, PID.5, PID.10, DGD.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.63, A:M.210, A:V.269, A:Y.270, A:Y.270, A:Y.270, A:Y.270, A:Y.302 Water bridges: A:Y.270 PID.10: 25 residues within 4Å: Chain A: L.41, L.181, W.186, H.229, A.232, I.233, I.236, G.240, V.241, T.242, Y.247, V.250, N.251, L.254, I.258, V.266, F.301, F.304, K.305, V.308, Q.309, Q.312 Ligands: CLA.2, PID.7, PID.9 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.181, A:W.186, A:W.186, A:I.233, A:I.236, A:Y.247, A:V.250, A:L.254, A:I.258, A:V.266, A:F.304, A:K.305, A:V.308, A:Q.309 Hydrogen bonds: A:T.242 Water bridges: A:Q.309 pi-Stacking: A:F.301 PID.15: 20 residues within 4Å: Chain B: F.17, W.23, N.25, F.28, L.29, P.120, A.121, M.123, K.124, A.132, E.133, Y.136, A.200, S.203, I.207 Ligands: CLA.13, PID.16, PID.18, DGD.23, DGD.24 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.17, B:W.23, B:F.28, B:F.28, B:F.28, B:F.28, B:F.28, B:P.120, B:K.124, B:K.124, B:Y.136, B:I.207 Hydrogen bonds: B:K.124, B:S.203 PID.16: 20 residues within 4Å: Chain B: I.27, F.28, Q.30, A.31, P.32, D.116, K.118, V.119, Y.122, M.123, I.207, M.210 Chain C: L.292, A.296 Ligands: CLA.13, PID.15, PID.20, PID.21, DGD.23, DGD.24 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.27, B:I.27, B:F.28, B:P.32, B:K.118, B:V.119, B:Y.122, B:Y.122, C:L.292, C:A.296 PID.17: 19 residues within 4Å: Chain B: M.47, I.48, M.50, G.51, V.104, M.105, V.107, Y.108, Y.136, L.140, K.143, L.222, K.223, A.226 Ligands: CLA.13, PID.18, PID.20, PID.21, DGD.23 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.107, B:Y.108, B:Y.108, B:Y.108, B:L.140, B:A.226 PID.18: 27 residues within 4Å: Chain B: W.23, N.24, H.66, A.69, I.70, I.73, G.78, V.79, T.80, W.85, V.88, N.89, L.92, I.96, E.101, V.104, F.139, F.142, K.143, V.146, K.147, Q.150, Q.201, L.204 Ligands: CLA.13, PID.15, PID.17 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.23, B:W.23, B:I.73, B:W.85, B:V.88, B:L.92, B:I.96, B:V.104, B:F.139, B:F.142, B:K.143, B:K.143, B:K.147 Hydrogen bonds: B:T.80, B:K.147, B:Q.201 PID.19: 20 residues within 4Å: Chain B: A.31, L.35, P.37, A.40, F.180, I.184, W.186, Y.191, M.192, P.282, L.283, M.285, F.286, A.294, A.298 Ligands: CLA.14, PID.20, PID.22, DGD.23, DGD.24 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.35, B:I.184, B:Y.191, B:Y.191, B:Y.191, B:P.282, B:M.285, B:F.286, B:F.286 PID.20: 16 residues within 4Å: Chain B: I.44, M.47, V.190, Y.191, K.193, P.196, I.281, N.284, M.285 Chain C: L.283 Ligands: CLA.14, PID.16, PID.17, PID.19, DGD.23, DGD.24 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.196, B:I.281 Hydrogen bonds: B:N.284 PID.21: 17 residues within 4Å: Chain B: L.59, K.60, A.63, M.210, I.211, M.213, G.214, V.266, M.267, V.269, Y.270, Y.302 Ligands: CLA.14, PID.16, PID.17, PID.22, DGD.24 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.63, B:V.269, B:Y.270, B:Y.302 Water bridges: B:Y.270 pi-Stacking: B:Y.270 PID.22: 25 residues within 4Å: Chain B: L.41, L.181, W.186, H.229, A.232, I.233, I.236, G.240, V.241, T.242, Y.247, V.250, N.251, L.254, I.258, V.266, F.301, F.304, K.305, V.308, Q.309, Q.312 Ligands: CLA.14, PID.19, PID.21 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.181, B:W.186, B:W.186, B:I.233, B:I.236, B:Y.247, B:V.250, B:L.254, B:I.258, B:V.266, B:F.304, B:K.305, B:V.308, B:Q.309 Hydrogen bonds: B:T.242 Water bridges: B:Q.309 pi-Stacking: B:F.301 PID.27: 21 residues within 4Å: Chain C: F.17, V.21, W.23, N.25, F.28, L.29, P.120, A.121, M.123, K.124, A.132, E.133, Y.136, A.200, S.203, I.207 Ligands: CLA.25, PID.28, PID.30, DGD.35, DGD.36 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.17, C:V.21, C:W.23, C:F.28, C:F.28, C:F.28, C:F.28, C:F.28, C:P.120, C:K.124, C:K.124, C:Y.136, C:I.207 Hydrogen bonds: C:K.124, C:S.203 PID.28: 20 residues within 4Å: Chain A: L.292, A.296 Chain C: I.27, F.28, Q.30, A.31, P.32, D.116, K.118, V.119, Y.122, M.123, I.207, M.210 Ligands: CLA.25, PID.27, PID.32, PID.33, DGD.35, DGD.36 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.27, C:F.28, C:P.32, C:K.118, C:V.119, C:Y.122, C:Y.122, A:A.296 PID.29: 19 residues within 4Å: Chain C: M.47, I.48, M.50, G.51, V.104, M.105, V.107, Y.108, Y.136, L.140, K.143, L.222, K.223, A.226 Ligands: CLA.25, PID.30, PID.32, PID.33, DGD.35 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.107, C:Y.108, C:Y.108, C:Y.108, C:L.140, C:A.226 PID.30: 27 residues within 4Å: Chain C: W.23, N.24, H.66, A.69, I.70, I.73, G.78, V.79, T.80, W.85, V.88, N.89, L.92, I.96, E.101, V.104, F.139, F.142, K.143, V.146, K.147, Q.150, Q.201, L.204 Ligands: CLA.25, PID.27, PID.29 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:W.23, C:W.23, C:I.73, C:W.85, C:V.88, C:L.92, C:I.96, C:V.104, C:F.139, C:F.142, C:K.143, C:K.143, C:K.147 Hydrogen bonds: C:T.80, C:Q.201 PID.31: 20 residues within 4Å: Chain C: A.31, L.35, P.37, A.40, F.180, I.184, W.186, Y.191, M.192, P.282, L.283, M.285, F.286, A.294, A.298 Ligands: CLA.26, PID.32, PID.34, DGD.35, DGD.36 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.35, C:I.184, C:Y.191, C:Y.191, C:Y.191, C:P.282, C:M.285, C:F.286, C:F.286 PID.32: 17 residues within 4Å: Chain A: S.280, L.283 Chain C: I.44, M.47, V.190, Y.191, K.193, P.196, I.281, N.284, M.285 Ligands: CLA.26, PID.28, PID.29, PID.31, DGD.35, DGD.36 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.196, C:I.281 Hydrogen bonds: C:N.284 PID.33: 17 residues within 4Å: Chain C: L.59, K.60, A.63, M.210, I.211, M.213, G.214, V.266, M.267, V.269, Y.270, Y.302 Ligands: CLA.26, PID.28, PID.29, PID.34, DGD.36 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.63, C:M.210, C:V.269, C:Y.270, C:Y.302 Water bridges: C:Y.270 pi-Stacking: C:Y.270 PID.34: 24 residues within 4Å: Chain C: L.41, W.186, H.229, A.232, I.233, I.236, G.240, V.241, T.242, Y.247, V.250, N.251, L.254, I.258, V.266, F.301, F.304, K.305, V.308, Q.309, Q.312 Ligands: CLA.26, PID.31, PID.33 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.186, C:W.186, C:I.233, C:I.236, C:Y.247, C:V.250, C:L.254, C:I.258, C:V.266, C:F.304, C:K.305, C:V.308, C:Q.309 Hydrogen bonds: C:T.242 Water bridges: C:Q.309 pi-Stacking: C:F.301

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

DGD.11: 18 residues within 4Å: Chain A: P.32, I.44, M.47, V.107, Y.108, V.111, S.112, T.115, P.120, E.133, Y.136, E.137 Ligands: CLA.1, PID.3, PID.4, PID.5, PID.7, PID.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.32, A:I.44, A:V.107, A:Y.108, A:V.111, A:V.111 Hydrogen bonds: A:E.133, A:Y.136, A:Y.136 DGD.12: 19 residues within 4Å: Chain A: Y.270, M.273, A.274, T.277, P.282, N.295, A.298, K.299, Y.302 Chain C: D.22, N.24, N.25, G.26 Ligands: CLA.2, PID.3, PID.4, PID.7, PID.8, PID.9 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Y.270, A:M.273, A:A.274 Hydrogen bonds: A:Y.270, A:N.295, A:K.299, A:Y.302, C:D.22, C:G.26 Water bridges: A:Y.270, C:D.22, C:N.24 DGD.23: 17 residues within 4Å: Chain B: P.32, I.44, V.107, Y.108, V.111, S.112, T.115, P.120, E.133, Y.136, E.137 Ligands: CLA.13, PID.15, PID.16, PID.17, PID.19, PID.20 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.32, B:I.44, B:V.107, B:Y.108, B:V.111, B:V.111 Hydrogen bonds: B:E.133, B:Y.136, B:Y.136 DGD.24: 19 residues within 4Å: Chain A: D.22, N.24, N.25, G.26 Chain B: Y.270, M.273, A.274, T.277, P.282, N.295, A.298, K.299, Y.302 Ligands: CLA.14, PID.15, PID.16, PID.19, PID.20, PID.21 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:M.273, B:A.274 Hydrogen bonds: B:Y.270, B:N.295, B:K.299, B:Y.302, A:D.22, A:G.26 Water bridges: B:Y.270, A:D.22, A:N.24 DGD.35: 18 residues within 4Å: Chain C: P.32, I.44, M.47, V.107, Y.108, V.111, S.112, T.115, P.120, E.133, Y.136, E.137 Ligands: CLA.25, PID.27, PID.28, PID.29, PID.31, PID.32 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:P.32, C:I.44, C:V.107, C:Y.108, C:V.111, C:V.111 Hydrogen bonds: C:E.133, C:Y.136, C:Y.136 DGD.36: 20 residues within 4Å: Chain B: D.22, N.24, N.25, G.26 Chain C: M.210, Y.270, M.273, A.274, T.277, P.282, N.295, A.298, K.299, Y.302 Ligands: CLA.26, PID.27, PID.28, PID.31, PID.32, PID.33 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:Y.270, C:M.273, C:A.274 Hydrogen bonds: C:Y.270, C:N.295, C:K.299, C:Y.302, B:D.22, B:N.24, B:G.26 Water bridges: C:Y.270, B:D.22, B:N.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hofmann, E. et al., Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein from Amphidinium carterae. Science (1996)

Release Date

1997-08-20

Peptides

PERIDININ-CHLOROPHYLL PROTEIN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
O

PERIDININ-CHLOROPHYLL PROTEIN