SMTL ID : 1f99.1

CRYSTAL STRUCTURE OF R-PHYCOCYANIN FROM POLYSIPHONIA AT 2.4 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-6-6-mer

Ligands

12 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 27 residues within 4Å: Chain A: V.59, T.66, P.72, N.73, Y.74, S.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, M.94, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Chain D: R.57, I.67, Y.74, T.75, S.76, M.79 24 PLIP interactions: 21 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:V.59, A:K.83, A:K.83, A:I.88, A:Y.90, A:L.111, A:I.118, A:F.122, A:L.124, A:W.128, A:W.128, A:Y.129 Hydrogen bonds: A:N.73, A:S.75, A:R.86, A:D.87, D:T.75 Water bridges: A:K.83, A:K.83, A:K.83, D:T.75 Salt bridges: A:K.83, A:R.86, D:R.57 CYC.2: 17 residues within 4Å: Chain B: N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, L.113, L.120, T.122, P.123, S.126, V.127 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.78, B:I.88, B:L.113, B:L.120, B:V.127 Hydrogen bonds: B:N.72, B:N.72, B:R.84, B:D.85 CYC.4: 25 residues within 4Å: Chain C: V.59, T.66, P.72, N.73, Y.74, S.75, G.80, K.83, C.84, R.86, D.87, 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, S.76, M.79 22 PLIP interactions: 3 interactions with chain F, 19 interactions with chain C Hydrophobic interactions: F:Y.74, C:V.59, C:T.66, C:N.73, C:K.83, C:K.83, C:Y.90, C:L.111, C:F.122, C:W.128, C:Y.129 Hydrogen bonds: F:T.75, C:N.73, C:S.75, C:R.86, C:D.87, C:Y.129 Salt bridges: F:R.57, C:K.83, C:R.86 Water bridges: C:K.83, C:K.83 CYC.5: 20 residues within 4Å: Chain D: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, Y.117, L.120, T.122, P.123, S.126, V.127 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:R.78, D:A.81, D:I.88, D:L.113, D:T.122, D:V.127 Hydrogen bonds: D:N.72, D:N.72, D:R.84, D:D.85 Salt bridges: D:R.77, D:R.84 CYC.7: 26 residues within 4Å: Chain B: R.57, I.67, T.75, S.76, M.79 Chain E: V.59, T.66, P.72, N.73, Y.74, S.75, G.80, K.83, C.84, R.86, D.87, Y.90, M.94, Y.110, L.111, L.115, I.118, F.122, L.124, W.128, Y.129 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: E:V.59, E:T.66, E:N.73, E:K.83, E:Y.90, E:L.111, E:L.115, E:F.122, E:L.124, E:W.128, E:Y.129 Hydrogen bonds: E:N.73, E:S.75, E:R.86, E:D.87, B:T.75 Salt bridges: E:K.83, E:R.86, B:R.57 Water bridges: B:T.75 CYC.8: 19 residues within 4Å: Chain F: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, Y.117, L.120, T.122, S.126, V.127 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:R.78, F:A.81, F:I.88, F:I.88, F:L.113, F:L.120, F:T.122, F:V.127 Hydrogen bonds: F:N.72, F:N.72, F:R.84, F:D.85 Salt bridges: F:R.77, F:R.84 CYC.10: 27 residues within 4Å: Chain G: V.59, T.66, P.72, N.73, Y.74, S.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, M.94, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Chain J: R.57, I.67, Y.74, T.75, S.76, M.79 25 PLIP interactions: 22 interactions with chain G, 3 interactions with chain J Hydrophobic interactions: G:V.59, G:K.83, G:K.83, G:I.88, G:Y.90, G:L.111, G:I.118, G:F.122, G:L.124, G:W.128, G:W.128, G:Y.129 Hydrogen bonds: G:N.73, G:S.75, G:R.86, G:D.87, G:Y.129, J:T.75 Water bridges: G:K.83, G:K.83, G:K.83, J:T.75 Salt bridges: G:K.83, G:R.86, J:R.57 CYC.11: 17 residues within 4Å: Chain H: N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, L.113, L.120, T.122, P.123, S.126, V.127 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:R.78, H:I.88, H:L.113, H:L.120, H:V.127 Hydrogen bonds: H:N.72, H:N.72, H:R.84, H:D.85 CYC.13: 25 residues within 4Å: Chain I: V.59, T.66, P.72, N.73, Y.74, S.75, G.80, K.83, C.84, R.86, D.87, Y.90, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Chain L: R.57, I.67, Y.74, T.75, S.76, M.79 21 PLIP interactions: 18 interactions with chain I, 3 interactions with chain L Hydrophobic interactions: I:V.59, I:T.66, I:N.73, I:K.83, I:K.83, I:Y.90, I:L.111, I:F.122, I:W.128, I:Y.129, L:Y.74 Hydrogen bonds: I:N.73, I:S.75, I:R.86, I:D.87, L:T.75 Water bridges: I:K.83, I:K.83 Salt bridges: I:K.83, I:R.86, L:R.57 CYC.14: 20 residues within 4Å: Chain J: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, Y.117, L.120, T.122, P.123, S.126, V.127 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:R.78, J:A.81, J:I.88, J:L.113, J:T.122, J:V.127 Hydrogen bonds: J:N.72, J:N.72, J:R.84, J:D.85 Salt bridges: J:R.77, J:R.84 CYC.16: 26 residues within 4Å: Chain H: R.57, I.67, T.75, S.76, M.79 Chain K: V.59, T.66, P.72, N.73, Y.74, S.75, G.80, K.83, C.84, R.86, D.87, Y.90, M.94, Y.110, L.111, L.115, I.118, F.122, L.124, W.128, Y.129 21 PLIP interactions: 18 interactions with chain K, 3 interactions with chain H Hydrophobic interactions: K:V.59, K:T.66, K:N.73, K:K.83, K:Y.90, K:L.111, K:L.115, K:F.122, K:L.124, K:W.128, K:Y.129 Hydrogen bonds: K:N.73, K:S.75, K:R.86, K:D.87, K:Y.129, H:T.75 Salt bridges: K:K.83, K:R.86, H:R.57 Water bridges: H:T.75 CYC.17: 19 residues within 4Å: Chain L: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, Y.117, L.120, T.122, S.126, V.127 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:R.78, L:A.81, L:I.88, L:I.88, L:L.113, L:L.120, L:T.122, L:V.127 Hydrogen bonds: L:N.72, L:N.72, L:R.84, L:D.85 Salt bridges: L:R.77, L:R.84

6 x PEB: PHYCOERYTHROBILIN(Covalent)

PEB.3: 18 residues within 4Å: Chain A: N.21, L.24, Q.25, N.28 Chain B: N.35, K.36, L.38, D.39, V.40, V.142, N.143, T.148, P.149, A.150, G.151, C.153 Chain G: R.33, D.145 16 PLIP interactions: 2 interactions with chain A, 12 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: A:L.24, A:Q.25, B:N.35, B:K.36, B:L.38, B:V.40, B:P.149, B:P.149 Hydrogen bonds: B:N.35, B:N.35, B:D.39, B:T.148, B:P.149, B:G.151, G:R.33 pi-Cation interactions: G:R.33 PEB.6: 19 residues within 4Å: Chain C: L.24, Q.25, N.28 Chain D: N.35, K.36, L.38, D.39, V.40, V.142, N.143, D.144, T.148, P.149, A.150, G.151, C.153 Chain K: R.33, D.145, N.148 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:N.35, D:K.36, D:L.38, D:V.40, D:P.149, C:L.24, C:Q.25 Hydrogen bonds: D:N.35, D:D.39, D:D.39, D:P.149, D:G.151 PEB.9: 21 residues within 4Å: Chain E: N.21, L.24, Q.25, N.28 Chain F: N.35, K.36, L.38, D.39, V.40, V.142, N.143, D.144, T.145, T.148, P.149, A.150, G.151, C.153 Chain I: R.33, D.145, N.148 18 PLIP interactions: 3 interactions with chain I, 13 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: I:R.33, F:N.35, F:K.36, F:L.38, F:L.38, F:V.40, F:P.149, E:L.24, E:Q.25 Water bridges: I:D.145, F:N.143 pi-Cation interactions: I:R.33 Hydrogen bonds: F:N.35, F:K.36, F:D.39, F:D.39, F:P.149, F:G.151 PEB.12: 18 residues within 4Å: Chain A: R.33, D.145 Chain G: N.21, L.24, Q.25, N.28 Chain H: N.35, K.36, L.38, D.39, V.40, V.142, N.143, T.148, P.149, A.150, G.151, C.153 16 PLIP interactions: 2 interactions with chain A, 2 interactions with chain G, 12 interactions with chain H Hydrogen bonds: A:R.33, H:N.35, H:N.35, H:D.39, H:D.39, H:P.149, H:G.151 pi-Cation interactions: A:R.33 Hydrophobic interactions: G:L.24, G:Q.25, H:N.35, H:K.36, H:L.38, H:V.40, H:P.149, H:P.149 PEB.15: 19 residues within 4Å: Chain E: R.33, D.145, N.148 Chain I: L.24, Q.25, N.28 Chain J: N.35, K.36, L.38, D.39, V.40, V.142, N.143, D.144, T.148, P.149, A.150, G.151, C.153 11 PLIP interactions: 9 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:N.35, J:K.36, J:L.38, J:V.40, J:P.149, I:L.24, I:Q.25 Hydrogen bonds: J:N.35, J:D.39, J:P.149, J:G.151 PEB.18: 21 residues within 4Å: Chain C: R.33, D.145, N.148 Chain K: N.21, L.24, Q.25, N.28 Chain L: N.35, K.36, L.38, D.39, V.40, V.142, N.143, D.144, T.145, T.148, P.149, A.150, G.151, C.153 17 PLIP interactions: 2 interactions with chain K, 13 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: K:L.24, K:Q.25, L:N.35, L:K.36, L:L.38, L:L.38, L:V.40, L:P.149, C:R.33 Hydrogen bonds: L:N.35, L:K.36, L:D.39, L:P.149, L:G.151 Water bridges: L:N.143, L:T.148 pi-Cation interactions: C:R.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, T. et al., Crystal structure of R-phycocyanin and possible energy transfer pathways in the phycobilisome. Biophys.J. (2001)

Release Date

2001-07-09

Peptides

R-PHYCOCYANIN: ACEGIK
R-PHYCOCYANIN: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
K

E
M

G
A

I
K

K
M

B
B

D
L

F
N

H
B

J
L

L
N

R-PHYCOCYANIN

R-PHYCOCYANIN