SMTL ID : 1ktp.3 (4 other biounits)

Crystal structure of c-phycocyanin of synechococcus vulcanus at 1.6 angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-oligomer

Ligands

3 x BLA: BILIVERDINE IX ALPHA(Covalent)

BLA.1: 26 residues within 4Å: Chain A: V.59, T.66, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Chain D: R.57, I.67, Y.74, T.75, N.76, M.79 28 PLIP interactions: 4 interactions with chain D, 24 interactions with chain A Hydrophobic interactions: D:Y.74, A:V.59, A:T.66, A:K.83, A:K.83, A:I.88, A:Y.90, A:L.111, A:I.118, A:F.122, A:F.122, A:L.124, A:W.128, A:W.128, A:Y.129 Hydrogen bonds: D:T.75, D:N.76, A:A.75, A:R.86, A:Y.129 Salt bridges: D:R.57, A:K.83, A:R.86 Water bridges: A:S.72, A:S.72, A:S.72 pi-Stacking: A:Y.90 pi-Cation interactions: A:R.86 BLA.4: 26 residues within 4Å: Chain C: V.59, T.66, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Chain F: R.57, I.67, Y.74, T.75, N.76, M.79 28 PLIP interactions: 24 interactions with chain C, 4 interactions with chain F Hydrophobic interactions: C:V.59, C:T.66, C:K.83, C:K.83, C:I.88, C:Y.90, C:L.111, C:I.118, C:F.122, C:F.122, C:L.124, C:W.128, C:W.128, C:Y.129, F:Y.74 Hydrogen bonds: C:A.75, C:R.86, C:Y.129, F:T.75, F:N.76 Water bridges: C:S.72, C:S.72, C:S.72 Salt bridges: C:K.83, C:R.86, F:R.57 pi-Stacking: C:Y.90 pi-Cation interactions: C:R.86 BLA.7: 26 residues within 4Å: Chain B: R.57, I.67, Y.74, T.75, N.76, M.79 Chain E: V.59, T.66, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 28 PLIP interactions: 4 interactions with chain B, 24 interactions with chain E Hydrophobic interactions: B:Y.74, E:V.59, E:T.66, E:K.83, E:K.83, E:I.88, E:Y.90, E:L.111, E:I.118, E:F.122, E:F.122, E:L.124, E:W.128, E:W.128, E:Y.129 Hydrogen bonds: B:T.75, B:N.76, E:A.75, E:R.86, E:Y.129 Salt bridges: B:R.57, E:K.83, E:R.86 Water bridges: E:S.72, E:S.72, E:S.72 pi-Stacking: E:Y.90 pi-Cation interactions: E:R.86

6 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.2: 21 residues within 4Å: Chain B: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:R.78, B:A.81, B:I.88, B:Y.92, B:L.113, B:T.116, B:L.120, B:P.123 Hydrogen bonds: B:R.84 Water bridges: B:R.77, B:R.77, B:R.78 Salt bridges: B:R.77, B:R.77, B:R.84 pi-Cation interactions: B:R.84 CYC.3: 20 residues within 4Å: Chain A: N.21, L.24, Q.25, D.28 Chain B: K.32, N.35, K.36, L.38, D.39, R.43, A.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, M.157 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:N.35, B:K.36, B:L.38, B:L.38, B:I.148, A:L.24, A:Q.25 Hydrogen bonds: B:N.35, B:D.39, B:T.149, B:T.149, B:G.151 Water bridges: B:T.149, A:K.32, A:K.32 CYC.5: 21 residues within 4Å: Chain D: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:R.78, D:A.81, D:I.88, D:Y.92, D:L.113, D:T.116, D:L.120, D:P.123 Hydrogen bonds: D:R.84 Water bridges: D:R.77, D:R.77, D:R.78 Salt bridges: D:R.77, D:R.77, D:R.84 pi-Cation interactions: D:R.84 CYC.6: 20 residues within 4Å: Chain C: N.21, L.24, Q.25, D.28 Chain D: K.32, N.35, K.36, L.38, D.39, R.43, A.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, M.157 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:N.35, D:K.36, D:L.38, D:L.38, D:I.148, C:L.24, C:Q.25 Hydrogen bonds: D:N.35, D:D.39, D:T.149, D:T.149, D:G.151 Water bridges: D:T.149, C:K.32, C:K.32 CYC.8: 21 residues within 4Å: Chain F: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:R.78, F:A.81, F:I.88, F:Y.92, F:L.113, F:T.116, F:L.120, F:P.123 Hydrogen bonds: F:R.84 Water bridges: F:R.77, F:R.77, F:R.78 Salt bridges: F:R.77, F:R.77, F:R.84 pi-Cation interactions: F:R.84 CYC.9: 20 residues within 4Å: Chain E: N.21, L.24, Q.25, D.28 Chain F: K.32, N.35, K.36, L.38, D.39, R.43, A.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, M.157 15 PLIP interactions: 11 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:N.35, F:K.36, F:L.38, F:L.38, F:I.148, E:L.24, E:Q.25 Hydrogen bonds: F:N.35, F:D.39, F:T.149, F:T.149, F:G.151 Water bridges: F:T.149, E:K.32, E:K.32

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Adir, N. et al., Refined structure of c-phycocyanin from the cyanobacterium Synechococcus vulcanus at 1.6 A: insights into the role of solvent molecules in thermal stability and co-factor structure. Biochim.Biophys.Acta (2002)

Release Date

2002-03-06

Peptides

C-PHYCOCYANIN ALPHA SUBUNIT: ACE
C-PHYCOCYANIN BETA SUBUNIT: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

C-PHYCOCYANIN ALPHA SUBUNIT

C-PHYCOCYANIN BETA SUBUNIT

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