Research workbench
State transition supercomplex psi-lhci-lhcii from double phosphatase mutant PPH1;PBCP of green alga chlamydomonas reinhardtii
Analyse State transition supercomplex psi-lhci-lhcii from double phosphatase mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DZ7
- Type
- protein
- Length
- 5,998 residues
- Chains
- 29
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem I P700 chlorophyll a apoprotein A1; Photosystem I P700 chlorophyll a…
- EC
- 1.97.1.12
- UniProt
- P12154, P09144, Q00914, Q39615, P12352, P12356, P14224, P13352, A8IFG7, P59777, P14225, A8IL32, A8JCL6, Q05093, A8IKC8, A8JF10, Q75VZ0, Q75VY8, Q75VY6, Q84Y02, Q75VY7, A8ITV3, Q93WE0, Q93WL4, Q93VE0, Q9ZSJ4
- Ligands
- CLA, BCR, CHL, LHG, LUT, XAT, LMG, NEX, LMU, SF4, PQN, DGD
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 27 distinct chains · 52% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 741 | 60% helix, 5% strand | P12154 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 60% helix, 3% strand | P09144 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 10% helix, 20% strand | Q00914 |
| D | Photosystem I reaction center subunit II, chloroplastic | protein | 143 | 15% helix, 23% strand | Q39615 |
| E | Photosystem I reaction center subunit IV, chloroplastic | protein | 63 | 0% helix, 37% strand | P12352 |
| F | Photosystem I reaction center subunit III, chloroplastic | protein | 165 | 56% helix, 5% strand | P12356 |
| G | Photosystem I reaction center subunit V, chloroplastic | protein | 94 | 57% helix, 2% strand | P14224 |
| H | Photosystem I reaction center subunit VI, chloroplastic | protein | 100 | 45% helix, 2% strand | P13352 |
| I | Photosystem I reaction center subunit VIII | protein | 42 | 55% helix, 2% strand | A8IFG7 |
| J | Photosystem I reaction center subunit IX | protein | 41 | 71% helix, 2% strand | P59777 |
| K | Photosystem I reaction center subunit psak, chloroplastic | protein | 86 | 50% helix, 7% strand | P14225 |
| L | Psi subunit V | protein | 159 | 58% helix, 4% strand | A8IL32 |
| O | Photosystem I subunit O | protein | 97 | 56% helix, 0% strand | A8JCL6 |
| a, 1 | Chlorophyll a-B binding protein, chloroplastic | protein | 194 | 49% helix, 2% strand | Q05093 |
| 2 | Chlorophyll a-B binding protein, chloroplastic | protein | 217 | 56% helix, 0% strand | A8IKC8 |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 220 | 48% helix, 0% strand | A8JF10 |
| 4 | Chlorophyll a-B binding protein, chloroplastic | protein | 210 | 52% helix, 1% strand | Q75VZ0 |
| 5 | Chlorophyll a-B binding protein, chloroplastic | protein | 227 | 45% helix, 4% strand | Q75VY8 |
| 6 | Chlorophyll a-B binding protein, chloroplastic | protein | 230 | 42% helix, 6% strand | Q75VY6 |
| 7 | Chlorophyll a-B binding protein, chloroplastic | protein | 213 | 55% helix, 1% strand | Q84Y02 |
| 8 | Chlorophyll a-B binding protein, chloroplastic | protein | 217 | 54% helix, 0% strand | Q75VY7 |
| 9 | Chlorophyll a-B binding protein, chloroplastic | protein | 183 | 50% helix, 0% strand | A8ITV3 |
| X, W | Chlorophyll a-B binding protein, chloroplastic | protein | 220 | 52% helix, 2% strand | Q93WE0 |
| Y | Chlorophyll a-B binding protein, chloroplastic | protein | 220 | 52% helix, 2% strand | Q93WL4 |
| Z | Chlorophyll a-B binding protein, chloroplastic | protein | 232 | 49% helix, 1% strand | Q93VE0 |
| U | Chlorophyll a-B binding protein, chloroplastic | protein | 219 | 52% helix, 2% strand | Q93WL4 |
| V | Chlorophyll a-B binding protein, chloroplastic | protein | 238 | 46% helix, 2% strand | Q9ZSJ4 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 298 copies · chains A, B, F, J, 3, 7, K, O, L, I, H, G, 9, 1, 2, V, a, 4, 8, 5, 6, X, Y, Z, U, W
- BCR · Beta-carotene · ligand · 40 copies · chains A, O, B, J, F, G, 9, I, 2, K, L, H, a, 1, 3, 5, 4, 6, 7, 8
- CHL · Chlorophyll B · ligand · 36 copies · chains X, Z, Y, U, W, V
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 27 copies · chains A, B, 1, I, 2, 9, H, L, O, a, 4, 8, 3, 5, 7, 6, X, Y, Z, U, V, W
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 22 copies · chains a, 1, 2, 3, 4, 5, 6, 7, 8, 9, X, Y, Z, U, V, W
- 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 · ligand · 16 copies · chains a, 1, 2, 3, 4, 5, 6, 7, 8, 9, X, Y, O, Z, U, V, W
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 11 copies · chains A, J, 7, H, L, 2, B, F, 4, 6, 8, 1, 9, V
- 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 · ligand · 8 copies · chains 5, 6, 4, X, Y, Z, U, V, W
- LMU · Dodecyl-alpha-D-maltoside · ligand · 7 copies · chains A, 3, K, G, 1, 5, 6, 4, 8
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.85 | 0.86 | 85 | CLA |
| 2 | 1043 | 0.81 | 0.82 | 105 | CLA, DGD |
| 3 | 646 | 0.80 | 0.85 | 63 | empty |
| 4 | 1025 | 0.75 | 0.77 | 117 | CLA, LHG |
| 5 | 1100 | 0.74 | 0.77 | 102 | CLA, LHG, LMG |
Interfaces
66 interfaces between chains.
- A–B · 3590 Ų buried · 51 hydrogen bonds · protein-protein
- H–L · 2062 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1697 Ų buried · 28 hydrogen bonds · protein-protein
- B–G · 1294 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 1189 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 modified, 1 covalent (disulfide, phosphorylation, covalent ligand).
Compared structures
- 7DZ7 · State transition supercomplex PSI-LHCI-LHCII from double phosphatase mutant pph1;pbcp of… · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P12154
- Every structure of UniProt P09144
- Every structure of UniProt Q00914
- Every structure of UniProt Q39615
- Every structure of UniProt P12352
- Every structure of UniProt P12356
- Every structure of UniProt P14224
- Every structure of UniProt P13352
- Every structure of UniProt A8IFG7
- Every structure of UniProt P59777
- Every structure of UniProt P14225
- Every structure of UniProt A8IL32
- Every structure of UniProt A8JCL6
- Every structure of UniProt Q05093
- Every structure of UniProt A8IKC8
- Every structure of UniProt A8JF10
- Every structure of UniProt Q75VZ0
- Every structure of UniProt Q75VY8
- Every structure of UniProt Q75VY6
- Every structure of UniProt Q84Y02
- Every structure of UniProt Q75VY7
- Every structure of UniProt A8ITV3
- Every structure of UniProt Q93WE0
- Every structure of UniProt Q93WL4
- Every structure of UniProt Q93VE0
- Every structure of UniProt Q9ZSJ4
- Elsewhere: RCSB PDB 7DZ7 · PDBe 7DZ7 · UniProt P12154 · UniProt P09144 · UniProt Q00914 · UniProt Q39615 · UniProt P12352 · UniProt P12356 · UniProt P14224 · UniProt P13352 · UniProt A8IFG7 · UniProt P59777 · UniProt P14225 · UniProt A8IL32 · UniProt A8JCL6 · UniProt Q05093 · UniProt A8IKC8 · UniProt A8JF10 · UniProt Q75VZ0 · UniProt Q75VY8 · UniProt Q75VY6 · UniProt Q84Y02 · UniProt Q75VY7 · UniProt A8ITV3 · UniProt Q93WE0 · UniProt Q93WL4 · UniProt Q93VE0 · UniProt Q9ZSJ4
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