SMTL ID : 3pl9.1

Crystal structure of spinach minor light-harvesting complex CP29 at 2.80 angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

9 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 13 residues within 4Å: Chain A: F.92, R.93, C.95, E.96, H.99, R.202, M.205, V.206, L.209 Ligands: CLA.2, CLA.7, CLA.13, XAT.15 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:F.92, A:H.99, A:R.202, A:R.202, A:M.205, A:V.206, A:L.209 Salt bridges: A:R.202 pi-Cation interactions: A:R.202 Metal complexes: A:E.96 CLA.2: 7 residues within 4Å: Chain A: R.91, F.92, C.95, H.99 Ligands: CLA.1, CLA.7, XAT.15 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:F.92 Hydrogen bonds: A:R.91 Salt bridges: A:R.91, A:R.91 pi-Stacking: A:H.99 Metal complexes: A:H.99 CLA.3: 17 residues within 4Å: Chain A: W.102, L.105, L.108, G.109, T.112, V.113, L.116, T.117, A.124, E.128, S.134, Y.135, L.136 Ligands: CHL.4, CLA.8, XAT.15, NEX.16 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.102, A:V.113, A:L.116, A:A.124, A:Y.135, A:Y.135, A:Y.135, A:L.136 Hydrogen bonds: A:L.136 Water bridges: A:G.137 pi-Stacking: A:Y.135, A:Y.135 Metal complexes: H2O.3 CLA.7: 20 residues within 4Å: Chain A: R.91, E.94, C.95, I.98, H.99, W.102, E.151, V.152, I.155, G.156, E.159, F.160, R.162, N.163 Ligands: CLA.1, CLA.2, CHL.4, CHL.5, XAT.15, HTG.18 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:I.98, A:W.102, A:I.155, A:E.159, A:F.160, A:N.163 Hydrogen bonds: A:H.99 Salt bridges: A:R.91, A:R.162 Metal complexes: A:E.159 CLA.8: 18 residues within 4Å: Chain A: R.101, M.104, L.105, Y.173, P.174, G.175, F.178, D.179, L.183, A.184, L.193, Q.194, A.196, E.197, H.200 Ligands: CLA.3, CHL.6, LUT.14 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:R.101, A:M.104, A:L.105, A:P.174, A:L.183, A:A.184, A:L.193, A:Q.194, A:A.196, A:E.197, A:H.200 Hydrogen bonds: A:G.175 pi-Cation interactions: A:R.101 Metal complexes: A:E.197 CLA.9: 9 residues within 4Å: Chain A: I.192, L.195, A.196, K.199, H.200, L.203 Ligands: CLA.10, CLA.13, G3P.17 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:K.199, A:K.199, A:L.203 Salt bridges: A:K.199 pi-Cation interactions: A:K.199 CLA.10: 6 residues within 4Å: Chain A: L.108, H.200, L.203 Ligands: CLA.9, CLA.11, LUT.14 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:L.108, A:L.203 Metal complexes: A:H.200 CLA.11: 16 residues within 4Å: Chain A: V.206, L.209, G.210, V.213, Q.214, V.217, T.218, N.225, H.229, T.236, T.237, I.238 Ligands: CLA.10, CHL.12, CLA.13, LUT.14 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:V.206, A:L.209, A:V.213, A:V.217, A:H.229 Hydrogen bonds: A:I.238 CLA.13: 10 residues within 4Å: Chain A: L.195, K.199, R.202, L.203, V.206 Ligands: CLA.1, CLA.9, CLA.11, XAT.15, G3P.17 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:L.195, A:L.195, A:K.199, A:V.206 Hydrogen bonds: A:R.202 Salt bridges: A:K.199 pi-Cation interactions: A:K.199, A:K.199, A:K.199

4 x CHL: CHLOROPHYLL B(Non-covalent)

CHL.4: 18 residues within 4Å: Chain A: G.125, E.128, S.133, L.140, F.142, M.144, L.147, I.150, E.151, I.155, Y.157, Q.161 Ligands: CLA.3, CHL.5, CHL.6, CLA.7, XAT.15, NEX.16 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:E.128, A:L.147, A:L.147, A:I.155 Metal complexes: H2O.1 CHL.5: 11 residues within 4Å: Chain A: Q.122, D.123, G.125, K.126, L.129, M.144, E.151, V.152 Ligands: CHL.4, CLA.7, XAT.15 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.129, A:E.151, A:V.152 Hydrogen bonds: A:G.125, A:K.126 Metal complexes: H2O.1 CHL.6: 16 residues within 4Å: Chain A: I.98, R.101, W.102, Y.157, I.158, Q.161, R.162, E.165, R.171, P.174, G.175, T.177, F.178 Ligands: CHL.4, CLA.8, NEX.16 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.157, A:I.158, A:R.162, A:E.165, A:P.174, A:F.178, A:F.178, A:F.178 Hydrogen bonds: A:R.101 pi-Stacking: A:F.178 pi-Cation interactions: A:R.162 Metal complexes: H2O.1 CHL.12: 11 residues within 4Å: Chain A: W.226, H.229, L.230, S.231, D.232, P.233, L.234, T.237, L.239 Ligands: CLA.11, LUT.14 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:P.233, A:P.233, A:L.234, A:T.237 Metal complexes: A:H.229

1 x LUT: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL(Non-covalent)

LUT.14: 22 residues within 4Å: Chain A: M.104, T.107, L.108, F.178, D.179, P.180, L.181, G.182, L.183, H.200, L.203, A.204, G.207, F.211, Q.214, P.222, N.225, W.226 Ligands: CLA.8, CLA.10, CLA.11, CHL.12 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:M.104, A:L.108, A:L.181, A:L.203, A:A.204, A:F.211, A:F.211, A:W.226, A:W.226, A:W.226 Hydrogen bonds: A:L.181, A:G.182, A:Q.214, A:P.222, A:W.226

1 x XAT: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL(Non-covalent)

XAT.15: 14 residues within 4Å: Chain A: H.99, A.106, W.121, A.124, M.205, F.208, L.209 Ligands: CLA.1, CLA.2, CLA.3, CHL.4, CHL.5, CLA.7, CLA.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.99, A:A.106, A:M.205, A:F.208, A:L.209 Hydrogen bonds: A:W.121

1 x NEX: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL(Non-covalent)

NEX.16: 8 residues within 4Å: Chain A: W.102, Y.135, V.154, Y.157, I.158 Ligands: CLA.3, CHL.4, CHL.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.102, A:V.154, A:Y.157, A:I.158 Hydrogen bonds: A:Y.135

1 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.17: 3 residues within 4Å: Chain A: K.199 Ligands: CLA.9, CLA.13 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.199

2 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)

HTG.18: 7 residues within 4Å: Chain A: V.152, L.153, G.156, Y.157, F.160, Q.161 Ligands: CLA.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.152, A:F.160, A:F.160 Hydrogen bonds: A:Q.161 HTG.19: 4 residues within 4Å: Chain A: E.165, L.166, D.167, K.170 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.166 Hydrogen bonds: A:E.165, A:D.167, A:K.170, A:K.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, X. et al., Structural insights into energy regulation of light-harvesting complex CP29 from spinach. Nat.Struct.Mol.Biol. (2011)

Release Date

2011-02-09

Peptides

Chlorophyll A-B binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Chlorophyll A-B binding protein

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