Research workbench
Dunaliella minimal psi complex
Analyse Dunaliella minimal psi complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QPH
- Type
- protein
- Length
- 2,790 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorophyll a-B binding protein, chloroplastic; LHC2; LHC4; Photosystem I P700…
- EC
- 1.97.1.12
- UniProt
- C1K003, C1K004, D0FXV2, D0FXZ0, D0FXW7, D0FXW0
- Ligands
- CLA, BCR, CHL, LHG, LUT, XAT, LMG, DGD, SF4, GSH, PQN, SQD, CL0, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 11 distinct chains · 49% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Chlorophyll a-B binding protein, chloroplastic | protein | 195 | 53% helix, 0% strand | C1K003 |
| 2 | LHC2 | protein | 211 | 48% helix, 0% strand | — |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 210 | 50% helix, 0% strand | C1K004 |
| 4 | LHC4 | protein | 211 | 49% helix, 2% strand | — |
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 739 | 57% helix, 4% strand | D0FXV2 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 734 | 56% helix, 1% strand | D0FXZ0 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 5% helix, 20% strand | D0FXW7 |
| D | Psad | protein | 142 | 12% helix, 18% strand | — |
| E | Psae | protein | 64 | 0% helix, 25% strand | — |
| F | Psaf | protein | 163 | 55% helix, 4% strand | — |
| J | Photosystem I reaction center subunit IX | protein | 41 | 54% helix, 0% strand | D0FXW0 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 132 copies · chains 1, 4, 2, 3, A, F, J, B
- BCR · Beta-carotene · ligand · 23 copies · chains 1, 4, F, 2, 3, A, B, J
- CHL · Chlorophyll B · ligand · 10 copies · chains 1, 4, 2, 3
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 5 copies · chains 1, 4, 2, A, B
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 4 copies · chains 1, 2, 3, 4
- 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 · 4 copies · chains 1, 2, 3, 4, F
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 4 copies · chains 1, B, 2
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 4 copies · chains 2, A, 4, J, B, C
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- GSH · Glutathione · ligand · 2 copies · chains B
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · chains 1
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- CA · Calcium ion · metal · chains B
- CAC · Cacodylate ion · additive · 6 copies · chains B, 1, 3, A, 4, F
- LMT · Dodecyl-beta-D-maltoside · additive · chains 2
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 | 1169 | 0.81 | 0.82 | 96 | CLA, DGD |
| 2 | 369 | 0.77 | 0.86 | 42 | CLA |
| 3 | 979 | 0.76 | 0.78 | 141 | CLA |
| 4 | 304 | 0.73 | 0.85 | 47 | CL0, CLA |
| 5 | 570 | 0.73 | 0.80 | 48 | empty |
Interfaces
26 interfaces between chains.
- A–B · 3526 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1701 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 1166 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1142 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 891 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6QPH · Dunaliella minimal PSI complex · the same entry in another collection · chain 1 against 1, 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 C1K003
- Every structure of UniProt C1K004
- Every structure of UniProt D0FXV2
- Every structure of UniProt D0FXZ0
- Every structure of UniProt D0FXW7
- Every structure of UniProt D0FXW0
- Elsewhere: RCSB PDB 6QPH · PDBe 6QPH · UniProt C1K003 · UniProt C1K004 · UniProt D0FXV2 · UniProt D0FXZ0 · UniProt D0FXW7 · UniProt D0FXW0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.