SMTL ID : 2uul.1 (1 other biounit)

Crystal structure of C-phycocyanin from Phormidium, Lyngbya spp. (Marine) and Spirulina sp. (Fresh water) shows two different ways of energy transfer between two hexamers.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-5-4-1-1-1-mer

Ligands

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

CYC.1: 23 residues within 4Å: Chain A: V.59, T.66, P.72, N.73, Y.74, A.75, R.79, K.83, C.84, R.86, D.87, Y.90, Y.110, L.111, F.122, L.124, W.128, Y.129 Chain D: R.57, I.67, Y.74, T.75, S.76 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:V.59, A:T.66, A:L.111, A:L.111, A:L.124, A:L.124, A:W.128, A:W.128, A:Y.129, D:Y.74 Hydrogen bonds: A:N.73, A:R.79, A:R.86, A:D.87, D:T.75 Salt bridges: A:K.83, A:R.86, D:R.57 pi-Stacking: A:Y.90 pi-Cation interactions: A:R.86 CYC.4: 23 residues within 4Å: Chain C: V.59, T.66, P.72, N.73, Y.74, A.75, R.79, K.83, C.84, R.86, D.87, Y.90, Y.110, L.111, F.122, L.124, W.128, Y.129 Chain F: R.57, I.67, Y.74, T.75, S.76 22 PLIP interactions: 19 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: C:V.59, C:T.66, C:L.111, C:L.111, C:F.122, C:L.124, C:L.124, C:W.128, C:W.128, C:Y.129, F:Y.74 Hydrogen bonds: C:N.73, C:R.86, C:D.87, C:Y.129, F:T.75 Salt bridges: C:R.79, C:K.83, C:R.86, F:R.57 pi-Stacking: C:Y.90 pi-Cation interactions: C:R.86 CYC.5: 19 residues within 4Å: Chain D: L.66, N.72, A.73, N.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, Y.117, L.120, T.122, S.126, V.127 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.66, D:A.81, D:I.88, D:Y.92, D:L.120, D:T.122, D:V.127 Hydrogen bonds: D:N.72, D:R.84, D:D.85 Salt bridges: D:R.84 pi-Cation interactions: D:R.84 CYC.7: 23 residues within 4Å: Chain B: R.57, I.67, Y.74, T.75, S.76 Chain E: V.59, T.66, P.72, N.73, Y.74, A.75, R.79, K.83, C.84, R.86, D.87, Y.90, Y.110, L.111, F.122, L.124, W.128, Y.129 20 PLIP interactions: 3 interactions with chain B, 17 interactions with chain E Hydrophobic interactions: B:Y.74, E:V.59, E:T.66, E:K.83, E:L.111, E:L.111, E:F.122, E:L.124, E:W.128 Hydrogen bonds: B:T.75, E:N.73, E:R.86, E:D.87, E:Y.129 Salt bridges: B:R.57, E:R.79, E:K.83, E:R.86 pi-Stacking: E:Y.90 pi-Cation interactions: E:R.86 CYC.8: 18 residues within 4Å: Chain F: L.66, N.72, A.73, N.77, R.78, C.82, R.84, D.85, M.86, I.88, R.108, C.109, Y.117, L.120, T.122, P.123, S.126, V.127 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:L.66, F:N.72, F:I.88, F:L.120, F:T.122, F:P.123, F:V.127 Hydrogen bonds: F:N.72, F:R.84, F:D.85, F:T.122 Salt bridges: F:R.84 pi-Cation interactions: F:R.84 CYC.9: 17 residues within 4Å: Chain E: F.28 Chain F: A.32, N.35, D.39, N.42, V.142, N.143, D.144, I.148, T.149, P.150, G.151, D.152, C.153 Chain I: Q.33, D.145, A.148 12 PLIP interactions: 3 interactions with chain I, 9 interactions with chain F Hydrophobic interactions: I:A.148, F:N.42, F:V.142, F:I.148, F:T.149 Hydrogen bonds: I:Q.33, I:D.145, F:D.39, F:T.149, F:T.149, F:G.151, F:C.153 CYC.10: 22 residues within 4Å: Chain G: V.59, T.66, P.72, N.73, Y.74, A.75, R.79, K.83, C.84, R.86, D.87, Y.90, Y.91, Y.110, L.111, L.124, W.128, Y.129 Chain J: R.57, I.67, T.75, S.76 19 PLIP interactions: 17 interactions with chain G, 2 interactions with chain J Hydrophobic interactions: G:T.66, G:K.83, G:Y.91, G:L.111, G:L.111, G:L.124, G:W.128, G:W.128 Hydrogen bonds: G:N.73, G:R.86, G:D.87, G:Y.129, J:T.75 Salt bridges: G:R.79, G:K.83, G:R.86, J:R.57 pi-Stacking: G:Y.90 pi-Cation interactions: G:R.86 CYC.11: 20 residues within 4Å: Chain H: L.59, L.66, N.72, A.73, N.77, R.78, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, Y.117, L.120, T.122, S.126, V.127 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:L.59, H:L.66, H:Y.92, H:L.113, H:L.120, H:L.120, H:V.127 Hydrogen bonds: H:N.72, H:N.77, H:R.84, H:D.85 pi-Cation interactions: H:R.84 CYC.12: 18 residues within 4Å: Chain A: Q.33, D.145, A.148 Chain G: I.24, F.28 Chain H: A.32, N.35, K.36, D.39, N.42, V.142, N.143, D.144, I.148, T.149, P.150, G.151, C.153 13 PLIP interactions: 8 interactions with chain H, 2 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: H:N.42, H:V.142, H:I.148, H:T.149, G:I.24, G:F.28, A:A.148 Hydrogen bonds: H:D.39, H:T.149, H:T.149, H:G.151, A:Q.33, A:D.145 CYC.13: 23 residues within 4Å: Chain I: V.59, T.66, P.72, N.73, Y.74, A.75, R.79, K.83, C.84, R.86, D.87, Y.90, Y.110, L.111, F.122, L.124, W.128, Y.129 Chain L: R.57, I.67, Y.74, T.75, S.76 21 PLIP interactions: 4 interactions with chain L, 17 interactions with chain I Hydrophobic interactions: L:I.67, L:Y.74, I:V.59, I:T.66, I:K.83, I:Y.90, I:L.111, I:L.111, I:L.124, I:L.124, I:W.128 Hydrogen bonds: L:T.75, I:N.73, I:R.86, I:D.87, I:Y.129 Salt bridges: L:R.57, I:K.83, I:R.86 pi-Stacking: I:Y.90 pi-Cation interactions: I:R.86 CYC.14: 18 residues within 4Å: Chain J: L.59, L.66, N.72, A.73, N.77, R.78, C.82, R.84, D.85, I.88, R.108, L.113, Y.117, L.120, T.122, P.123, S.126, V.127 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:L.59, J:L.66, J:R.78, J:I.88, J:L.113, J:Y.117, J:L.120, J:P.123, J:V.127 Hydrogen bonds: J:N.72, J:N.77, J:R.84, J:D.85 Salt bridges: J:R.84 pi-Cation interactions: J:R.84 CYC.15: 14 residues within 4Å: Chain E: Q.33, D.145 Chain I: F.28 Chain J: N.35, K.36, D.39, V.142, N.143, I.148, T.149, P.150, G.151, D.152, C.153 10 PLIP interactions: 8 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:I.148, J:T.149, I:F.28, I:F.28 Hydrogen bonds: J:D.39, J:D.39, J:T.149, J:T.149, J:G.151, J:C.153 CYC.16: 22 residues within 4Å: Chain H: R.57, I.67, T.75, S.76 Chain K: V.59, T.66, P.72, N.73, Y.74, A.75, R.79, K.83, C.84, R.86, D.87, Y.90, Y.110, L.111, F.122, L.124, W.128, Y.129 20 PLIP interactions: 18 interactions with chain K, 2 interactions with chain H Hydrophobic interactions: K:V.59, K:D.87, K:Y.90, K:L.111, K:L.111, K:L.124, K:L.124, K:W.128, K:Y.129 Hydrogen bonds: K:N.73, K:R.86, K:D.87, K:Y.129, H:T.75 Salt bridges: K:R.79, K:K.83, K:R.86, H:R.57 pi-Stacking: K:Y.90 pi-Cation interactions: K:R.86 CYC.17: 18 residues within 4Å: Chain L: L.66, N.72, A.73, N.77, R.78, C.82, R.84, D.85, M.86, I.88, R.108, L.113, Y.117, L.120, T.122, P.123, S.126, V.127 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:I.88, L:L.113, L:Y.117, L:L.120 Hydrogen bonds: L:N.72, L:N.77, L:R.84, L:D.85 Salt bridges: L:R.78, L:R.84 pi-Cation interactions: L:R.84 CYC.18: 17 residues within 4Å: Chain C: Q.33, D.145, V.148 Chain K: I.24, F.28 Chain L: N.35, K.36, D.39, N.42, V.142, N.143, D.144, I.148, T.149, P.150, G.151, C.153 12 PLIP interactions: 2 interactions with chain K, 8 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: K:I.24, K:F.28, L:K.36, L:I.148, L:T.149, C:V.148 Hydrogen bonds: L:D.39, L:T.149, L:T.149, L:G.151, L:C.153, C:Q.33

3 x BLA: BILIVERDINE IX ALPHA(Non-covalent)

BLA.2: 15 residues within 4Å: Chain B: L.66, N.72, A.73, R.78, C.82, R.84, D.85, M.86, I.88, R.108, Y.117, L.120, T.122, S.126, V.127 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:R.78, B:I.88, B:I.88, B:Y.117, B:T.122 Hydrogen bonds: B:N.72, B:R.84, B:D.85 Salt bridges: B:R.84 pi-Cation interactions: B:R.84 BLA.3: 17 residues within 4Å: Chain A: F.28 Chain B: N.35, K.36, D.39, N.42, V.142, D.144, I.148, T.149, P.150, G.151, D.152, C.153 Chain G: Q.33, D.145, A.148, E.149 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain G Hydrophobic interactions: B:N.35, B:K.36, B:D.39, B:I.148, B:T.149, G:A.148, G:E.149 Hydrogen bonds: B:N.35, B:D.39, B:T.149, B:T.149, B:G.151, G:Q.33, G:D.145 BLA.6: 16 residues within 4Å: Chain C: I.24, F.28 Chain D: N.35, K.36, D.39, N.42, V.142, I.148, T.149, P.150, G.151, D.152, C.153 Chain K: Q.33, D.145, A.148 13 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D, 3 interactions with chain K Hydrophobic interactions: C:I.24, C:F.28, C:F.28, D:N.35, D:N.42, D:I.148, K:A.148 Hydrogen bonds: D:N.35, D:D.39, D:G.151, D:C.153, K:Q.33, K:D.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Satyanarayana, L. et al., Crystal Structure of C-Phycocyanin from Phormidium, Lyngbya Spp. (Marine) and Spirulina Sp. (Fresh Water) Shows Two Different Ways of Energy Transfer between Twohexamers. To be Published

Release Date

2008-05-27

Peptides

C-PHYCOCYANIN ALPHA CHAIN: AEGIK
C-PHYCOCYANIN BETA CHAIN: BFJL
C-PHYCOCYANIN ALPHA CHAIN: C
C-PHYCOCYANIN BETA CHAIN: D
C-PHYCOCYANIN BETA CHAIN: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

G
G

I
I

K
K

B
B

F
F

J
J

L
L

C
C

D
D

H
H

C-PHYCOCYANIN ALPHA CHAIN

C-PHYCOCYANIN BETA CHAIN

C-PHYCOCYANIN ALPHA CHAIN

C-PHYCOCYANIN BETA CHAIN

C-PHYCOCYANIN BETA CHAIN

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