SMTL ID : 5tjf.1

The crystal structure of Allophycocyanin from the red algae Gracilaria chilensis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-oligomer

Ligands

6 x CYC: PHYCOCYANOBILIN(Covalent)(Non-covalent)

CYC.1: 32 residues within 4Å: Chain A: L.57, V.64, N.70, A.71, M.76, T.79, C.80, R.82, D.83, L.84, Y.86, Y.87, L.90, I.106, G.107, V.111, M.114, Y.115, L.118, T.120, P.121, G.124, V.125, G.128 Chain D: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Ligands: PEG.3 19 PLIP interactions: 11 interactions with chain A, 8 interactions with chain D Hydrophobic interactions: A:L.57, A:L.84, A:Y.87, A:I.106, A:T.120, D:L.61, D:T.75 Hydrogen bonds: A:N.70, A:D.83, D:Y.62, D:Y.62, D:Y.62, D:T.66 Water bridges: A:R.82, D:T.66, D:T.66 Salt bridges: A:R.82 pi-Stacking: A:Y.86 pi-Cation interactions: A:R.82 CYC.10: 27 residues within 4Å: Chain B: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126, A.129 Ligands: CL.26, CL.27 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.60, B:R.77, B:A.80, B:L.85, B:Y.87, B:Y.88, B:Y.91, B:V.108, B:V.108, B:L.112, B:Y.116, B:L.119, B:V.121, B:V.121, B:A.125 Hydrogen bonds: B:D.84, B:Y.116 Water bridges: B:R.83 Salt bridges: B:R.76, B:R.77, B:R.83 pi-Cation interactions: B:R.83 CYC.29: 32 residues within 4Å: Chain C: L.57, V.64, N.70, A.71, M.76, T.79, C.80, R.82, D.83, L.84, Y.86, Y.87, L.90, I.106, G.107, V.111, M.114, Y.115, L.118, T.120, P.121, G.124, V.125, G.128 Chain F: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Ligands: PEG.31 19 PLIP interactions: 8 interactions with chain F, 11 interactions with chain C Hydrophobic interactions: F:L.61, F:T.75, C:L.57, C:L.84, C:Y.87, C:I.106, C:T.120 Hydrogen bonds: F:Y.62, F:Y.62, F:Y.62, F:T.66, C:N.70, C:D.83 Water bridges: F:T.66, F:T.66, C:R.82 Salt bridges: C:R.82 pi-Stacking: C:Y.86 pi-Cation interactions: C:R.82 CYC.38: 27 residues within 4Å: Chain D: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126, A.129 Ligands: CL.54, CL.55 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:L.60, D:R.77, D:A.80, D:L.85, D:Y.87, D:Y.88, D:Y.91, D:V.108, D:V.108, D:L.112, D:Y.116, D:L.119, D:V.121, D:V.121, D:A.125 Hydrogen bonds: D:D.84, D:Y.116 Water bridges: D:R.83 Salt bridges: D:R.76, D:R.77, D:R.83 pi-Cation interactions: D:R.83 CYC.57: 32 residues within 4Å: Chain B: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain E: L.57, V.64, N.70, A.71, M.76, T.79, C.80, R.82, D.83, L.84, Y.86, Y.87, L.90, I.106, G.107, V.111, M.114, Y.115, L.118, T.120, P.121, G.124, V.125, G.128 Ligands: PEG.59 19 PLIP interactions: 11 interactions with chain E, 8 interactions with chain B Hydrophobic interactions: E:L.57, E:L.84, E:Y.87, E:I.106, E:T.120, B:L.61, B:T.75 Hydrogen bonds: E:N.70, E:D.83, B:Y.62, B:Y.62, B:Y.62, B:T.66 Water bridges: E:R.82, B:T.66, B:T.66 Salt bridges: E:R.82 pi-Stacking: E:Y.86 pi-Cation interactions: E:R.82 CYC.66: 27 residues within 4Å: Chain F: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126, A.129 Ligands: CL.82, CL.83 22 PLIP interactions: 22 interactions with chain F Hydrophobic interactions: F:L.60, F:R.77, F:A.80, F:L.85, F:Y.87, F:Y.88, F:Y.91, F:V.108, F:V.108, F:L.112, F:Y.116, F:L.119, F:V.121, F:V.121, F:A.125 Hydrogen bonds: F:D.84, F:Y.116 Water bridges: F:R.83 Salt bridges: F:R.76, F:R.77, F:R.83 pi-Cation interactions: F:R.83

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

PEG.2: 6 residues within 4Å: Chain A: G.68, G.69, N.70, L.118, G.119 Chain D: K.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.68, A:N.70 Water bridges: A:N.70 PEG.3: 5 residues within 4Å: Chain A: M.76 Chain D: A.57, L.61, Y.62 Ligands: CYC.1 No protein-ligand interaction detected (PLIP) PEG.11: 6 residues within 4Å: Chain B: Q.32, T.33, E.35, L.36, R.39 Ligands: NA.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.39, B:R.39 PEG.12: 7 residues within 4Å: Chain B: Y.116, N.117, G.120, V.121, P.122, I.123 Ligands: NA.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.120, B:I.123 PEG.30: 6 residues within 4Å: Chain C: G.68, G.69, N.70, L.118, G.119 Chain F: K.53 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.68, C:N.70 Water bridges: C:N.70 PEG.31: 5 residues within 4Å: Chain C: M.76 Chain F: A.57, L.61, Y.62 Ligands: CYC.29 No protein-ligand interaction detected (PLIP) PEG.39: 6 residues within 4Å: Chain D: Q.32, T.33, E.35, L.36, R.39 Ligands: NA.45 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.39, D:R.39 PEG.40: 7 residues within 4Å: Chain D: Y.116, N.117, G.120, V.121, P.122, I.123 Ligands: NA.52 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.120, D:I.123 PEG.58: 6 residues within 4Å: Chain B: K.53 Chain E: G.68, G.69, N.70, L.118, G.119 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.68, E:N.70 Water bridges: E:N.70 PEG.59: 5 residues within 4Å: Chain B: A.57, L.61, Y.62 Chain E: M.76 Ligands: CYC.57 No protein-ligand interaction detected (PLIP) PEG.67: 6 residues within 4Å: Chain F: Q.32, T.33, E.35, L.36, R.39 Ligands: NA.73 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.39, F:R.39 PEG.68: 7 residues within 4Å: Chain F: Y.116, N.117, G.120, V.121, P.122, I.123 Ligands: NA.80 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.120, F:I.123

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

NA.4: 4 residues within 4Å: Chain A: V.65, G.73, E.74, T.77 Ligand excluded by PLIP NA.5: 1 residues within 4Å: Chain A: S.18 Ligand excluded by PLIP NA.6: 3 residues within 4Å: Chain A: P.121, I.122, S.123 Ligand excluded by PLIP NA.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.8: 4 residues within 4Å: Chain A: L.48, K.51, Q.52, Q.55 Ligand excluded by PLIP NA.13: 3 residues within 4Å: Chain B: P.68 Chain E: Y.86 Chain F: G.16 Ligand excluded by PLIP NA.14: 1 residues within 4Å: Chain B: Y.62 Ligand excluded by PLIP NA.15: 2 residues within 4Å: Chain B: R.83, Y.87 Ligand excluded by PLIP NA.16: 2 residues within 4Å: Chain B: R.17, D.20 Ligand excluded by PLIP NA.17: 6 residues within 4Å: Chain B: Q.32, T.33, G.34, E.35, L.36 Ligands: PEG.11 Ligand excluded by PLIP NA.18: 2 residues within 4Å: Chain B: A.42, T.43 Ligand excluded by PLIP NA.19: 1 residues within 4Å: Chain B: T.115 Ligand excluded by PLIP NA.20: 1 residues within 4Å: Chain B: R.17 Ligand excluded by PLIP NA.21: 2 residues within 4Å: Chain B: N.22, K.26 Ligand excluded by PLIP NA.22: 2 residues within 4Å: Chain B: R.37, E.148 Ligand excluded by PLIP NA.23: 1 residues within 4Å: Chain B: N.10 Ligand excluded by PLIP NA.24: 1 residues within 4Å: Ligands: PEG.12 Ligand excluded by PLIP NA.32: 4 residues within 4Å: Chain C: V.65, G.73, E.74, T.77 Ligand excluded by PLIP NA.33: 1 residues within 4Å: Chain C: S.18 Ligand excluded by PLIP NA.34: 3 residues within 4Å: Chain C: P.121, I.122, S.123 Ligand excluded by PLIP NA.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.36: 4 residues within 4Å: Chain C: L.48, K.51, Q.52, Q.55 Ligand excluded by PLIP NA.41: 3 residues within 4Å: Chain A: Y.86 Chain B: G.16 Chain D: P.68 Ligand excluded by PLIP NA.42: 1 residues within 4Å: Chain D: Y.62 Ligand excluded by PLIP NA.43: 2 residues within 4Å: Chain D: R.83, Y.87 Ligand excluded by PLIP NA.44: 2 residues within 4Å: Chain D: R.17, D.20 Ligand excluded by PLIP NA.45: 6 residues within 4Å: Chain D: Q.32, T.33, G.34, E.35, L.36 Ligands: PEG.39 Ligand excluded by PLIP NA.46: 2 residues within 4Å: Chain D: A.42, T.43 Ligand excluded by PLIP NA.47: 1 residues within 4Å: Chain D: T.115 Ligand excluded by PLIP NA.48: 1 residues within 4Å: Chain D: R.17 Ligand excluded by PLIP NA.49: 2 residues within 4Å: Chain D: N.22, K.26 Ligand excluded by PLIP NA.50: 2 residues within 4Å: Chain D: R.37, E.148 Ligand excluded by PLIP NA.51: 1 residues within 4Å: Chain D: N.10 Ligand excluded by PLIP NA.52: 1 residues within 4Å: Ligands: PEG.40 Ligand excluded by PLIP NA.60: 4 residues within 4Å: Chain E: V.65, G.73, E.74, T.77 Ligand excluded by PLIP NA.61: 1 residues within 4Å: Chain E: S.18 Ligand excluded by PLIP NA.62: 3 residues within 4Å: Chain E: P.121, I.122, S.123 Ligand excluded by PLIP NA.63: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.64: 4 residues within 4Å: Chain E: L.48, K.51, Q.52, Q.55 Ligand excluded by PLIP NA.69: 3 residues within 4Å: Chain C: Y.86 Chain D: G.16 Chain F: P.68 Ligand excluded by PLIP NA.70: 1 residues within 4Å: Chain F: Y.62 Ligand excluded by PLIP NA.71: 2 residues within 4Å: Chain F: R.83, Y.87 Ligand excluded by PLIP NA.72: 2 residues within 4Å: Chain F: R.17, D.20 Ligand excluded by PLIP NA.73: 6 residues within 4Å: Chain F: Q.32, T.33, G.34, E.35, L.36 Ligands: PEG.67 Ligand excluded by PLIP NA.74: 2 residues within 4Å: Chain F: A.42, T.43 Ligand excluded by PLIP NA.75: 1 residues within 4Å: Chain F: T.115 Ligand excluded by PLIP NA.76: 1 residues within 4Å: Chain F: R.17 Ligand excluded by PLIP NA.77: 2 residues within 4Å: Chain F: N.22, K.26 Ligand excluded by PLIP NA.78: 2 residues within 4Å: Chain F: R.37, E.148 Ligand excluded by PLIP NA.79: 1 residues within 4Å: Chain F: N.10 Ligand excluded by PLIP NA.80: 1 residues within 4Å: Ligands: PEG.68 Ligand excluded by PLIP

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

CL.9: 2 residues within 4Å: Chain A: K.5, V.100 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain A: V.8, D.11, A.12 Chain B: R.107 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: R.76 Ligands: CYC.10 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: R.83, Y.87 Ligands: CYC.10 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain A: R.46 Chain B: Y.18, D.20 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain C: K.5, V.100 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain C: V.8, D.11, A.12 Chain D: R.107 Ligand excluded by PLIP CL.54: 2 residues within 4Å: Chain D: R.76 Ligands: CYC.38 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain D: R.83, Y.87 Ligands: CYC.38 Ligand excluded by PLIP CL.56: 3 residues within 4Å: Chain C: R.46 Chain D: Y.18, D.20 Ligand excluded by PLIP CL.65: 2 residues within 4Å: Chain E: K.5, V.100 Ligand excluded by PLIP CL.81: 4 residues within 4Å: Chain E: V.8, D.11, A.12 Chain F: R.107 Ligand excluded by PLIP CL.82: 2 residues within 4Å: Chain F: R.76 Ligands: CYC.66 Ligand excluded by PLIP CL.83: 3 residues within 4Å: Chain F: R.83, Y.87 Ligands: CYC.66 Ligand excluded by PLIP CL.84: 3 residues within 4Å: Chain E: R.46 Chain F: Y.18, D.20 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dagnino-Leone, J. et al., Structural models of the different trimers present in the core of phycobilisomes from Gracilaria chilensis based on crystal structures and sequences. PLoS ONE (2017)

Release Date

2017-05-24

Peptides

Allophycocyanin alpha subunit: ACE
Allophycocyanin beta subunit: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Allophycocyanin alpha subunit

Allophycocyanin beta subunit