SMTL ID : 3jbb.1

Characterization of red-shifted phycobiliprotein complexes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

12 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 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain F Hydrophobic interactions: 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, F:Y.73, F:T.75, F:Y.78 Hydrogen bonds: A:N.71, A:N.71, A:Q.80, A:R.83, F:Y.62, F:T.66, F:T.74 Water bridges: 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 19 PLIP interactions: 19 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 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 25 PLIP interactions: 6 interactions with chain B, 19 interactions with chain C Hydrophobic interactions: B:Y.73, B:T.75, B:Y.78, 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 Hydrogen bonds: B:Y.62, B:T.66, B:T.74, C:N.71, C:N.71, C:Q.80, C:R.83 Water bridges: C:R.83 Salt bridges: C:R.83 pi-Stacking: C:W.87 pi-Cation interactions: C:R.83 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 19 PLIP interactions: 19 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: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 24 PLIP interactions: 18 interactions with chain E, 6 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:Q.80, E:R.83, D:Y.62, D:T.66, D:T.74 Water bridges: E:R.83 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 19 PLIP interactions: 19 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 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 CYC.28: 27 residues within 4Å: Chain G: 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 L: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 26 PLIP interactions: 17 interactions with chain G, 9 interactions with chain L Hydrophobic interactions: G:A.72, G:Q.77, G:Q.80, G:Q.80, G:Y.85, G:Y.88, G:T.107, G:L.119, G:L.119, G:A.129, L:Y.73, L:T.75, L:Y.78 Hydrogen bonds: G:N.71, G:N.71, G:Q.80, G:R.83, L:Y.62, L:T.74 Salt bridges: G:R.83 pi-Stacking: G:W.87 pi-Cation interactions: G:R.83 Water bridges: L:T.66, L:T.66, L:T.66, L:T.66 CYC.31: 21 residues within 4Å: Chain H: 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 19 PLIP interactions: 19 interactions with chain H Hydrophobic interactions: H:R.77, H:A.80, H:L.85, H:Y.87, H:Y.87, H:Y.88, H:Y.91, H:L.112, H:L.119, H:V.121, H:V.121, H:P.122 Water bridges: H:R.76, H:R.76, H:R.77, H:R.83 Salt bridges: H:R.76, H:R.77, H:R.83 CYC.37: 28 residues within 4Å: Chain H: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain I: 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 27 PLIP interactions: 18 interactions with chain I, 9 interactions with chain H Hydrophobic interactions: I:A.72, I:Q.77, I:Q.80, I:Q.80, I:Y.85, I:W.87, I:Y.88, I:T.107, I:L.119, I:L.119, I:A.129, H:Y.73, H:T.75, H:Y.78 Hydrogen bonds: I:N.71, I:N.71, I:Q.80, I:R.83, H:Y.62, H:T.74 Salt bridges: I:R.83 pi-Stacking: I:W.87 pi-Cation interactions: I:R.83 Water bridges: H:T.66, H:T.66, H:T.66, H:T.66 CYC.40: 21 residues within 4Å: Chain J: 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 18 PLIP interactions: 18 interactions with chain J Hydrophobic interactions: J:R.77, J:A.80, J:L.85, J:Y.88, J:Y.91, J:L.112, J:V.121, J:V.121, J:P.122 Hydrogen bonds: J:R.83 Water bridges: J:R.76, J:R.76, J:R.77, J:R.83 Salt bridges: J:R.76, J:R.77, J:R.83 pi-Stacking: J:Y.87 CYC.46: 27 residues within 4Å: Chain J: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain K: 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 26 PLIP interactions: 9 interactions with chain J, 17 interactions with chain K Hydrophobic interactions: J:Y.73, J:T.75, J:Y.78, K:A.72, K:Q.77, K:Q.80, K:Q.80, K:Y.85, K:Y.88, K:T.107, K:L.119, K:L.119, K:A.129 Hydrogen bonds: J:Y.62, J:T.74, K:N.71, K:N.71, K:Q.80, K:R.83 Water bridges: J:T.66, J:T.66, J:T.66, J:T.66 Salt bridges: K:R.83 pi-Stacking: K:W.87 pi-Cation interactions: K:R.83 CYC.49: 21 residues within 4Å: Chain L: 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 L Hydrophobic interactions: L:R.77, L:A.80, L:L.85, L:Y.87, L:Y.88, L:Y.91, L:L.112, L:V.121, L:V.121, L:P.122 Hydrogen bonds: L:R.83 Water bridges: L:R.76, L:R.76, L:R.77, L:R.83, L:R.83 Salt bridges: L:R.76, L:R.77, L:R.83 pi-Stacking: L:Y.87

42 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 SO4.29: 3 residues within 4Å: Chain G: A.34, Q.35, R.38 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain G: S.142, A.143 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain H: D.20, G.21 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain H: P.122, I.123, S.124 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain H: E.35, R.39 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain H: T.50, K.53 Chain I: N.120 Ligand excluded by PLIP SO4.36: 1 residues within 4Å: Chain H: R.77 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain I: A.34, Q.35, R.38 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain I: S.142, A.143 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain J: D.20, G.21 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain J: P.122, I.123, S.124 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain J: E.35, R.39 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain J: T.50, K.53 Chain K: N.120 Ligand excluded by PLIP SO4.45: 1 residues within 4Å: Chain J: R.77 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain K: Q.35, R.38 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain K: S.142, A.143 Ligand excluded by PLIP SO4.50: 2 residues within 4Å: Chain L: D.20, G.21 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain L: P.122, I.123, S.124 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain L: E.35, R.39 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain G: N.120 Chain L: T.50, K.53 Ligand excluded by PLIP SO4.54: 1 residues within 4Å: Chain L: R.77 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Characterization of red-shifted phycobilisomes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris. Biochim.Biophys.Acta (2015)

Release Date

2015-11-11

Peptides

allophycocyanin subunit alpha-B: ACEGIK
allophycocyanin beta chain: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

B
B

D
D

F
F

H
H

J
J

L
L

allophycocyanin subunit alpha-B

allophycocyanin beta chain

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