SMTL ID : 6yq8.1

Crystal structure of native Phycocyanin from T. elongatus in spacegroup P63 at 1.8 Angstroms

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-1-1-mer

Ligands

3 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 24 residues within 4Å: Chain A: V.59, Y.60, 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.91, M.94, Y.110, L.111, L.115, I.118, F.122, L.124, W.128, Y.129 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.59, A:Y.60, A:T.66, A:K.83, A:Y.90, A:Y.91, A:I.118, A:F.122, A:W.128, A:W.128, A:W.128, A:Y.129 Hydrogen bonds: A:Q.73, A:A.75, A:R.86, A:D.87 Water bridges: A:S.72, A:S.72 Salt bridges: A:K.83, A:R.86 pi-Stacking: A:Y.90 pi-Cation interactions: A:R.86 CYC.7: 27 residues within 4Å: Chain B: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127, A.130 Ligands: EDO.17 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:R.78, B:A.81, B:I.88, B:L.113, B:L.120, B:T.122, B:A.130 Hydrogen bonds: B:R.84, B:D.85 Water bridges: B:R.77, B:R.77 Salt bridges: B:R.77, B:R.84 pi-Cation interactions: B:R.84 CYC.8: 22 residues within 4Å: Chain A: N.21, L.24, Q.25, D.28 Chain B: N.35, K.36, L.38, D.39, A.40, N.42, R.43, A.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, L.156, M.157 17 PLIP interactions: 3 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:L.24, A:Q.25, B:N.35, B:L.38, B:L.38, B:I.148, B:T.149 Water bridges: A:K.32, B:K.32, B:T.149, B:T.149 Hydrogen bonds: B:N.35, B:N.35, B:D.39, B:T.149, B:T.149, B:G.151

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: I.112, A.113, G.114, L.115, S.116, E.117 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.114, A:L.115, A:S.116, A:S.116, A:E.117, A:E.117 GOL.3: 7 residues within 4Å: Chain A: M.1, K.2, T.6, E.7, A.10 Chain B: M.1, R.108 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.1, B:R.108, A:M.1 GOL.9: 5 residues within 4Å: Chain B: N.42, R.43, N.146, G.147, I.148 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.43, B:R.43 Water bridges: B:D.39, B:D.39, B:S.46, B:N.146

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: D.28, F.31, K.32 Chain B: V.31, K.32, G.34, N.35 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.32 Water bridges: B:N.35, B:N.35, B:N.35, B:N.35 EDO.10: 8 residues within 4Å: Chain B: N.29, L.30, E.33, K.36, R.37, C.153, A.155, L.156 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.37 Water bridges: B:L.30, B:E.33, B:E.33, B:R.37, B:D.152, B:L.156 EDO.11: 8 residues within 4Å: Chain B: Q.11, A.12, R.15, E.17, F.18, L.19, T.20, Q.23 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.11, B:E.17, B:F.18, B:T.20, B:Q.23 EDO.12: 4 residues within 4Å: Chain B: A.80, A.81, L.83, R.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.84 Water bridges: B:A.81 EDO.14: 6 residues within 4Å: Chain B: D.106, L.110, N.111, R.166, A.169, A.170 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain B: A.155, S.158, E.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.158, B:E.159 Water bridges: B:S.158 EDO.17: 3 residues within 4Å: Chain B: L.113, T.116 Ligands: CYC.7 No protein-ligand interaction detected (PLIP)

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 5 residues within 4Å: Chain A: R.17, S.20, T.22, E.23, A.26 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.20 Water bridges: A:R.17, A:R.17, A:E.23 PGE.6: 6 residues within 4Å: Chain A: M.1, E.109 Chain B: M.1, L.2, S.103, D.107 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.1, B:D.107, A:M.1, A:E.109 PGE.13: 3 residues within 4Å: Chain B: A.140, I.141, D.144 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.144 Water bridges: B:R.43 PGE.15: 8 residues within 4Å: Chain B: K.7, G.100, D.101, S.102, D.106, G.162, Y.163, R.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.7, B:S.102 Water bridges: B:S.102, B:S.103, B:D.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sarrou, I. et al., C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening. Acta Crystallogr D Struct Biol (2021)

Release Date

2021-01-20

Peptides

C-phycocyanin alpha chain: A
C-phycocyanin beta chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C-phycocyanin alpha chain

C-phycocyanin beta chain

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