SMTL ID : 4po5.1 (1 other biounit)

Crystal structure of allophycocyanin B from Synechocystis PCC 6803

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-3-3-mer

Ligands

6 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 27 residues within 4Å: Chain A: L.58, Y.65, N.71, A.72, Q.77, Q.80, C.81, R.83, D.84, Y.85, W.87, Y.88, T.107, M.115, Y.116, L.119, V.121, G.125, M.126, A.129 Chain F: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 27 PLIP interactions: 7 interactions with chain F, 20 interactions with chain A Hydrophobic interactions: F:Y.73, F:T.75, F:Y.78, A:A.72, A:Q.77, A:Q.80, A:Q.80, A:Y.85, A:Y.88, A:T.107, A:L.119, A:L.119, A:A.129 Hydrogen bonds: F:Y.62, F:T.66, F:T.74, A:N.71, A:N.71, A:N.71, A:Q.80, A:R.83, A:D.84 Water bridges: F:T.66, A:R.83 Salt bridges: A:R.83 pi-Stacking: A:W.87 pi-Cation interactions: A:R.83 CYC.4: 21 residues within 4Å: Chain B: V.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, L.112, Y.116, L.119, V.121, P.122, S.125, T.126 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:R.77, B:A.80, B:L.85, B:Y.87, B:Y.87, B:Y.88, B:Y.91, B:L.112, B:L.119, B:V.121, B:V.121, B:P.122 Hydrogen bonds: B:D.84 Water bridges: B:R.76, B:R.76, B:R.77, B:R.83 Salt bridges: B:R.76, B:R.77, B:R.83 CYC.10: 28 residues within 4Å: Chain B: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain C: L.58, F.59, Y.65, N.71, A.72, Q.77, Q.80, C.81, R.83, D.84, Y.85, W.87, Y.88, T.107, M.115, Y.116, L.119, V.121, G.125, M.126, A.129 30 PLIP interactions: 20 interactions with chain C, 10 interactions with chain B Hydrophobic interactions: C:A.72, C:Q.77, C:Q.80, C:Q.80, C:Y.85, C:W.87, C:Y.88, C:T.107, C:L.119, C:L.119, C:A.129, B:Y.73, B:T.75, B:Y.78 Hydrogen bonds: C:N.71, C:N.71, C:N.71, C:Q.80, C:R.83, C:D.84, B:Y.62, B:T.74 Salt bridges: C:R.83 pi-Stacking: C:W.87 pi-Cation interactions: C:R.83 Water bridges: B:T.66, B:T.66, B:T.66, B:T.66, B:T.66 CYC.13: 21 residues within 4Å: Chain D: V.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, L.112, Y.116, L.119, V.121, P.122, S.125, T.126 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:R.77, D:A.80, D:L.85, D:Y.88, D:Y.91, D:L.112, D:V.121, D:V.121, D:P.122 Hydrogen bonds: D:R.83, D:D.84, D:Y.116 Water bridges: D:R.76, D:R.76, D:R.77, D:R.83 Salt bridges: D:R.76, D:R.77, D:R.83 pi-Stacking: D:Y.87 CYC.19: 27 residues within 4Å: Chain D: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain E: L.58, Y.65, N.71, A.72, Q.77, Q.80, C.81, R.83, D.84, Y.85, W.87, Y.88, T.107, M.115, Y.116, L.119, V.121, G.125, M.126, A.129 27 PLIP interactions: 20 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:A.72, E:Q.77, E:Q.80, E:Q.80, E:Y.85, E:Y.88, E:T.107, E:L.119, E:L.119, E:A.129, D:Y.73, D:T.75, D:Y.78 Hydrogen bonds: E:N.71, E:N.71, E:N.71, E:Q.80, E:R.83, E:D.84, D:Y.62, D:T.66, D:T.74 Water bridges: E:R.83, D:T.66 Salt bridges: E:R.83 pi-Stacking: E:W.87 pi-Cation interactions: E:R.83 CYC.22: 21 residues within 4Å: Chain F: V.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, L.112, Y.116, L.119, V.121, P.122, S.125, T.126 21 PLIP interactions: 21 interactions with chain F Hydrophobic interactions: F:R.77, F:A.80, F:L.85, F:Y.87, F:Y.88, F:Y.91, F:L.112, F:V.121, F:V.121, F:P.122 Hydrogen bonds: F:R.83, F:D.84 Water bridges: F:R.76, F:R.76, F:R.77, F:R.83, F:R.83 Salt bridges: F:R.76, F:R.77, F:R.83 pi-Stacking: F:Y.87

21 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: A.34, Q.35, R.38 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: S.142, A.143 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain B: D.20, G.21 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain B: P.122, I.123, S.124 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain B: E.35, R.39 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: T.50, K.53 Chain C: N.120 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain B: R.77 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain C: A.34, Q.35, R.38 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain C: S.142, A.143 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain D: D.20, G.21 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain D: P.122, I.123, S.124 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain D: E.35, R.39 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain D: T.50, K.53 Chain E: N.120 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Chain D: R.77 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain E: Q.35, R.38 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain E: S.142, A.143 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain F: D.20, G.21 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain F: P.122, I.123, S.124 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain F: E.35, R.39 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain A: N.120 Chain F: T.50, K.53 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain F: R.77 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, P.P. et al., The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-10-29

Peptides

Allophycocyanin subunit alpha-B: ACE
Allophycocyanin beta chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Allophycocyanin subunit alpha-B

Allophycocyanin beta chain

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