SMTL ID : 4lms.1

Light harvesting complex PC645 from the cryptophyte Chroomonas sp. CCMP270

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

hetero-1-2-1-mer

Ligands

2 x M1V: mesobiliverdin IX(alpha)(Covalent)

M1V.1: 23 residues within 4Å: Chain A: F.13, A.15, C.18, A.20, N.22, A.23, Q.24, Y.25, D.35, D.36, Q.37, C.38, K.40 Chain B: Y.18, G.20, G.21 Chain C: L.63, L.66, K.67 Chain D: P.64, A.65, I.67, S.68 24 PLIP interactions: 17 interactions with chain A, 4 interactions with chain D, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.13, A:F.13, A:F.13, A:F.13, A:A.15, A:A.20, A:N.22, A:Q.24, A:Y.25, D:P.64, D:P.64, D:I.67, C:L.63, C:L.66, B:Y.18 Hydrogen bonds: A:N.22, A:Q.24, A:Q.24, A:Y.25 Water bridges: A:N.22, A:K.40, D:S.68 Salt bridges: A:K.40 pi-Stacking: A:F.13 M1V.6: 24 residues within 4Å: Chain A: I.61, M.76, T.77, K.78 Chain B: P.64, A.65, I.67, S.68 Chain C: F.13, C.18, D.20, H.21, N.23, K.24, E.25, Y.26, D.37, E.38, C.39, C.40, K.42 Chain D: Y.18, G.20, G.21 24 PLIP interactions: 1 interactions with chain A, 18 interactions with chain C, 3 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: A:I.61, C:F.13, C:F.13, C:F.13, C:D.20, C:H.21, C:N.23, C:E.25, C:Y.26, B:P.64, B:I.67, D:Y.18 Hydrogen bonds: C:E.25, C:E.25, C:E.25, C:Y.26, D:Y.18 Water bridges: C:K.42, C:K.42, B:S.68 Salt bridges: C:H.21, C:K.42 pi-Stacking: C:F.13 pi-Cation interactions: C:H.21

2 x DBV: 15,16-DIHYDROBILIVERDIN(Covalent)

DBV.2: 26 residues within 4Å: Chain A: G.63, K.64, A.65, T.66, A.67, V.70, P.71, I.72, I.73, S.74 Chain B: C.50, I.51, D.54, S.57, G.58, C.61, G.132, I.133, A.136, T.137, A.140, F.141, S.146, N.147, Q.148 Ligands: DBV.7 23 PLIP interactions: 9 interactions with chain A, 11 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: A:T.66, A:A.67, A:V.70, A:V.70, A:P.71, A:I.73, B:A.136, B:T.137, B:F.141, B:Q.148 Hydrogen bonds: A:P.71, A:I.73, A:S.74, B:D.54, B:N.147, B:Q.148 Water bridges: B:R.129, B:R.129, B:A.136, B:T.145, D:K.150, D:K.150 Salt bridges: D:K.150 DBV.7: 22 residues within 4Å: Chain A: A.67, I.68 Chain B: N.147, Q.148, K.150 Chain C: E.65, K.67 Chain D: N.47, C.50, I.51, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, T.137, A.140, F.141 Ligands: DBV.2 21 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A, 11 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: B:Q.148, B:K.150, A:A.67, A:I.68, D:D.54, D:I.133, D:I.133, D:A.136, D:T.137, D:F.141, C:E.65 Hydrogen bonds: B:N.147, A:I.68, D:D.54, C:K.67 Water bridges: B:Q.148, B:K.150, D:D.54, D:R.129 Salt bridges: D:R.129 pi-Stacking: D:F.141

4 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.3: 22 residues within 4Å: Chain A: I.12, F.13, D.14, R.16, M.33, Q.37, C.38, V.39 Chain B: L.24, K.28, N.35, K.36, L.38, D.39, A.40, I.142, N.144, T.153, P.154, A.155, G.156, C.158 19 PLIP interactions: 12 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:N.35, B:K.36, B:L.38, B:N.144, B:T.153, B:P.154, A:I.12, A:D.14, A:V.39 Hydrogen bonds: B:K.28, B:N.35, B:D.39, B:T.153, B:P.154, B:G.156 Water bridges: A:R.16, A:R.16, A:R.16 Salt bridges: A:R.16 CYC.4: 23 residues within 4Å: Chain A: R.1, D.2, L.5 Chain B: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, G.126, N.127 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:R.78, B:A.81, B:L.113, B:L.120, B:V.122, A:D.2, A:L.5 Hydrogen bonds: B:R.84, B:D.85, A:D.2 Water bridges: B:R.77, B:R.77, B:R.84, B:T.116, A:R.1, A:D.2 Salt bridges: B:R.77, B:R.84 pi-Cation interactions: B:R.84 CYC.8: 24 residues within 4Å: Chain C: I.12, F.13, D.14, R.16, E.35, C.39, C.40, V.41 Chain D: L.24, K.28, N.35, K.36, L.38, D.39, A.40, F.141, I.142, N.144, L.151, T.153, P.154, A.155, G.156, C.158 26 PLIP interactions: 16 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:N.35, D:K.36, D:K.36, D:L.38, D:N.144, D:P.154, D:P.154, C:I.12, C:D.14, C:E.35, C:V.41 Hydrogen bonds: D:K.28, D:N.35, D:D.39, D:D.39, D:T.153, D:P.154, D:G.156 Water bridges: D:K.36, D:K.36, C:R.16, C:R.16, C:R.16, C:R.16, C:E.35 Salt bridges: C:R.16 CYC.9: 25 residues within 4Å: Chain C: K.1, D.2, L.5, R.6 Chain D: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, G.126, N.127, A.130 17 PLIP interactions: 4 interactions with chain C, 13 interactions with chain D Hydrophobic interactions: C:D.2, C:L.5, D:A.81, D:L.113, D:L.120, D:V.122, D:A.130 Hydrogen bonds: C:D.2, D:R.84, D:D.85 Water bridges: C:K.1, D:R.78, D:T.116 Salt bridges: D:R.77, D:R.78, D:R.84 pi-Cation interactions: D:R.84

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.5: 6 residues within 4Å: Chain A: V.41, M.43 Chain B: A.17, V.19, Y.95, S.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.108 P6G.10: 7 residues within 4Å: Chain C: V.43, M.45 Chain D: A.17, V.19, Y.95, L.98, S.99 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Y.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrop, S.J. et al., Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-06-18

Peptides

cryptophyte phycocyanin (alpha-1 chain): A
cryptophyte phycocyanin (beta chain): BD
cryptophyte phycocyanin (alpha-2 chain): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

cryptophyte phycocyanin (alpha-1 chain)

cryptophyte phycocyanin (beta chain)

cryptophyte phycocyanin (alpha-2 chain)