SMTL ID : 7t7u.1

Light Harvesting complex phycocyanin PC 630, from the cryptophyte Chroomonas sp. M1627

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-2-1-mer

Ligands

2 x M1V: mesobiliverdin IX(alpha)(Non-covalent)(Covalent)

M1V.1: 26 residues within 4Å: Chain A: F.14, N.16, C.19, E.20, V.21, K.23, N.24, N.25, Y.26, E.35, D.36, D.37, Q.38, C.39, K.41 Chain B: Y.14, G.16, G.17 Chain C: L.63, L.66 Chain D: P.60, A.61, I.63, S.64, P.65, Y.70 21 PLIP interactions: 1 interactions with chain D, 17 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: D:P.60, A:F.14, A:F.14, A:V.21, A:Y.26, C:L.63, B:Y.14 Hydrogen bonds: A:N.16, A:N.25, A:N.25, A:Y.26, B:Y.14 Water bridges: A:N.16, A:K.23, A:K.23, A:K.23, A:K.23, A:N.25 Salt bridges: A:K.23, A:K.41 pi-Stacking: A:F.14 M1V.6: 31 residues within 4Å: Chain A: I.62, L.64, G.76, V.77, T.78, K.79 Chain B: P.60, A.61, I.63, S.64, P.65, Y.70 Chain C: F.14, A.16, C.19, K.20, D.21, H.22, N.24, K.25, E.26, Y.27, E.36, D.37, D.38, Q.39, C.40, K.42 Chain D: Y.14, G.16, G.17 26 PLIP interactions: 2 interactions with chain A, 20 interactions with chain C, 2 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: A:I.62, A:L.64, C:F.14, C:F.14, C:D.21, C:H.22, C:N.24, C:E.26, C:Y.27, B:P.60, B:I.63, D:Y.14 Hydrogen bonds: C:H.22, C:E.26, C:E.26, C:E.26, C:Y.27, D:Y.14 Water bridges: C:H.22, C:S.23, C:E.26 Salt bridges: C:H.22, C:K.25, C:K.42 pi-Stacking: C:F.14, C:H.22

2 x AX9: DiCys-(15,16)-Dihydrobiliverdin(Covalent)

AX9.2: 29 residues within 4Å: Chain A: L.64, K.65, A.66, T.67, A.68, V.71, P.72, Q.73, I.74, S.75 Chain B: C.46, I.47, D.50, S.53, G.54, C.57, R.125, G.128, I.129, A.132, T.133, A.136, F.137, S.142, Q.143, Q.144 Chain D: C.46 Ligands: GOL.5, AX9.9 20 PLIP interactions: 7 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:T.67, A:V.71, A:P.72, A:I.74, B:I.129, B:A.132, B:T.133, B:F.137, B:Q.144 Hydrogen bonds: A:P.72, A:I.74, A:S.75, B:D.50, B:D.50, B:A.132, B:Q.143, B:Q.144 Water bridges: B:R.125, B:A.132, B:A.136 AX9.9: 24 residues within 4Å: Chain A: A.68, I.69 Chain B: Q.143, Q.144, K.146, L.147 Chain C: E.65, K.67 Chain D: N.43, C.46, I.47, D.50, S.53, G.54, C.57, E.58, R.125, I.129, A.132, T.133, A.136, F.137 Ligands: AX9.2, GOL.5 20 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C, 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: D:D.50, D:I.129, D:T.133, D:F.137, C:E.65, B:Q.144, B:K.146, A:A.68, A:I.69 Hydrogen bonds: D:D.50, D:D.50, B:Q.143, B:Q.143, B:Q.143, B:Q.144, A:I.69 Water bridges: D:R.125, C:K.67 Salt bridges: D:R.125 pi-Stacking: D:F.137

4 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.3: 26 residues within 4Å: Chain A: I.13, F.14, D.15, R.17, M.34, Q.38, C.39, V.40 Chain B: L.20, K.24, N.31, K.32, L.34, D.35, A.36, N.38, I.138, N.139, N.140, T.149, P.150, A.151, G.152, D.153, C.154, L.157 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: A:I.13, A:D.15, A:V.40, B:N.31, B:K.32, B:L.34, B:L.34, B:D.35, B:N.140, B:T.149, B:P.150, B:P.150 Hydrogen bonds: A:Q.38, B:K.24, B:N.31, B:D.35, B:T.149, B:P.150, B:G.152 Water bridges: A:R.17, B:N.31 CYC.4: 32 residues within 4Å: Chain A: I.2, K.3, K.4, D.5, Q.6, K.7 Chain B: V.52, M.55, L.62, N.68, C.69, R.73, R.74, A.77, C.78, R.80, D.81, A.82, I.84, I.85, Y.88, R.104, C.105, L.109, T.112, Y.113, L.116, V.118, P.119, G.122, N.123, A.126 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:R.74, B:A.77, B:I.84, B:Y.88, B:L.116, B:V.118, A:I.2 Hydrogen bonds: B:R.80, B:D.81, A:D.5, A:D.5, A:Q.6, A:Q.6 Water bridges: B:R.80 Salt bridges: B:R.73, B:R.80 pi-Cation interactions: B:R.80 CYC.7: 27 residues within 4Å: Chain C: I.13, F.14, D.15, R.17, M.35, Q.39, C.40, V.41 Chain D: L.20, K.24, N.31, K.32, L.34, D.35, A.36, N.38, F.137, I.138, N.140, L.147, T.149, P.150, A.151, G.152, D.153, C.154, L.157 18 PLIP interactions: 11 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:N.31, D:K.32, D:N.140, D:P.150, C:I.13, C:D.15, C:V.41 Hydrogen bonds: D:K.24, D:N.31, D:D.35, D:D.35, D:P.150, D:G.152, C:Q.39 Water bridges: D:K.32, C:R.17 Salt bridges: C:R.17 pi-Cation interactions: C:R.17 CYC.8: 31 residues within 4Å: Chain C: I.2, K.3, K.4, D.5, Q.6, K.7, A.8 Chain D: V.52, M.55, L.62, N.68, C.69, R.74, A.77, C.78, R.80, D.81, A.82, I.84, Y.88, R.104, C.105, L.109, T.112, Y.113, L.116, V.118, P.119, G.122, N.123, A.126 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:A.77, D:I.84, D:Y.88, D:L.116, D:V.118, D:V.118, D:A.126, C:I.2 Hydrogen bonds: D:R.80, D:D.81, C:D.5, C:Q.6, C:Q.6 Water bridges: D:R.80, C:Q.6, C:Q.6 Salt bridges: D:R.74, D:R.80 pi-Cation interactions: D:R.80

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 12 residues within 4Å: Chain B: S.42, N.43, C.46, F.137, K.146 Chain C: E.61 Chain D: C.46, S.49, D.50, S.53 Ligands: AX9.2, AX9.9 8 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: B:K.146, D:S.53, C:E.61 Water bridges: B:N.43, B:N.43, B:S.45, C:E.61, C:E.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michie, K.A. et al., Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins. Protein Sci. (2023)

Release Date

2023-02-15

Peptides

Phycoerythrin alpha subunit L1: A
Phycoerythrin beta subunit: BD
Phycoerythrin alpha subunit S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

Phycoerythrin alpha subunit L1

Phycoerythrin beta subunit

Phycoerythrin alpha subunit S1