MolNFT v1 · #171232 · protein
Dunaliella minimal photosystem I
6YXR · Chlorophyll a-B binding protein, chloroplastic: “Dunaliella minimal photosystem I”. Electron microscopy, 12 ligands (CLA, BCR, CHL), 20 pockets (best druggability 0.83). MolNFT v1 #171232 on GenesisL1: 3D structure, binding sites…
- PDB
- 6YXR
- Type
- protein
- Length
- 2,783 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorophyll a-B binding protein, chloroplastic; LHCA2; LHCA4; Photosystem I P700…
- EC
- 1.97.1.12
- UniProt
- C1K003, C1K004, D0FXV2, D0FXZ0, D0FXW7, D0FXW0
- Ligands
- CLA, BCR, CHL, LHG, LMG, LUT, XAT, SF4, PQN, 3PH, CL0, DGD
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 11 distinct chains · 52% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Chlorophyll a-B binding protein, chloroplastic | protein | 197 | 56% helix, 0% strand | C1K003 |
| 2 | LHCA2 | protein | 208 | 51% helix, 0% strand | — |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 210 | 49% helix, 0% strand | C1K004 |
| 4 | LHCA4 | protein | 211 | 45% helix, 2% strand | — |
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 739 | 60% helix, 4% strand | D0FXV2 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 730 | 59% helix, 3% strand | D0FXZ0 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 13% helix, 20% strand | D0FXW7 |
| D | Psad | protein | 141 | 17% helix, 23% strand | — |
| E | Psae | protein | 64 | 0% helix, 31% strand | — |
| F | Psaf | protein | 163 | 61% helix, 5% strand | — |
| J | Photosystem I reaction center subunit IX | protein | 40 | 70% helix, 3% strand | D0FXW0 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 134 copies · chains 1, 4, 2, 3, A, F, J, B
- BCR · Beta-carotene · ligand · 23 copies · chains 1, 2, 3, 4, A, B, F, J
- CHL · Chlorophyll B · ligand · 10 copies · chains 1, 4, 2, 3
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains 1, 4, 2, 3, A, B
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 5 copies · chains 2, 4, A, J, 3, 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
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, B
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · chains 3, A
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains B, C
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 | 1138 | 0.83 | 0.83 | 80 | CL0, CLA |
| 2 | 1149 | 0.77 | 0.79 | 95 | DGD |
| 3 | 734 | 0.72 | 0.78 | 62 | CLA |
| 4 | 691 | 0.72 | 0.78 | 87 | CLA |
| 5 | 755 | 0.69 | 0.76 | 78 | CLA |
Interfaces
25 interfaces between chains.
- A–B · 3564 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1622 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 1115 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1079 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 903 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6YXR · Dunaliella Minimal Photosystem I · 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 6YXR · PDBe 6YXR · UniProt C1K003 · UniProt C1K004 · UniProt D0FXV2 · UniProt D0FXZ0 · UniProt D0FXW7 · UniProt D0FXW0
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