Research workbench
Psi-lhci supercomplex from physcometrella patens
Analyse Psi-lhci supercomplex from physcometrella patens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L35
- Type
- protein
- Length
- 3,260 residues
- Chains
- 17
- 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
- Q8MFA3, Q8MFA2, Q6YXQ2, A9SRC8, A0A2K1IKE2, A0A2K1J0L9, A9SJ10, A9SL09, Q6YXR3, Q6YXM2, A9SFV4, A9S7M7, Q6YXK4, A0A2K1K0C7, A9T399, A9TEM8, A0A2K1KN29
- Ligands
- CLA, BCR, CHL, LHG, LUT, XAT, SF4, LMG, PQN, DGD
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 17 distinct chains · 51% 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 | 742 | 57% helix, 4% strand | Q8MFA3 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 733 | 60% helix, 2% strand | Q8MFA2 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 15% helix, 21% strand | Q6YXQ2 |
| D | Predicted protein psad | protein | 141 | 16% helix, 25% strand | A9SRC8 |
| E | Psae | protein | 62 | 5% helix, 29% strand | A0A2K1IKE2 |
| F | Psi-F | protein | 159 | 61% helix, 5% strand | A0A2K1J0L9 |
| G | Predicted protein psag | protein | 98 | 53% helix, 4% strand | A9SJ10 |
| H | Psah photosystem I reaction center subunit | protein | 90 | 34% helix, 2% strand | A9SL09 |
| I | Photosystem I reaction center subunit VIII | protein | 34 | 65% helix, 0% strand | Q6YXR3 |
| J | Photosystem I reaction center subunit IX | protein | 41 | 71% helix, 2% strand | Q6YXM2 |
| K | Psak | protein | 79 | 42% helix, 0% strand | A9SFV4 |
| L | Psi subunit V | protein | 159 | 55% helix, 4% strand | A9S7M7 |
| M | Photosystem I reaction center subunit XII | protein | 29 | 79% helix, 0% strand | Q6YXK4 |
| 2 | Chlorophyll a-B binding protein, chloroplastic | protein | 206 | 49% helix, 0% strand | A0A2K1K0C7 |
| 6 | Chlorophyll a-B binding protein, chloroplastic | protein | 192 | 48% helix, 0% strand | A9T399 |
| 3 | Chlorophyll a-B binding protein, chloroplastic | protein | 213 | 41% helix, 0% strand | A9TEM8 |
| 5 | Chlorophyll a-B binding protein, chloroplastic | protein | 202 | 52% helix, 1% strand | A0A2K1KN29 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 144 copies · chains A, B, F, J, 3, K, L, M, I, H, G, 6, 2, 5
- BCR · Beta-carotene · ligand · 26 copies · chains A, B, J, F, G, I, K, L, 2, 3, 5
- CHL · Chlorophyll B · ligand · 12 copies · chains 2, 3, 6, 5, G
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains A, B, 6, 2, 3, 5
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 4 copies · chains 2, 6, 3, 5
- 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 2, 6, 3, F, 5
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 3 copies · chains F, J, 2
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, 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 | 724 | 0.78 | 0.83 | 63 | DGD |
| 2 | 871 | 0.78 | 0.81 | 93 | CLA |
| 3 | 1021 | 0.76 | 0.78 | 112 | CLA |
| 4 | 834 | 0.73 | 0.77 | 73 | CLA, CHL |
| 5 | 578 | 0.71 | 0.79 | 63 | CLA |
Interfaces
40 interfaces between chains.
- A–B · 3572 Ų buried · 41 hydrogen bonds · protein-protein
- H–L · 1915 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1585 Ų buried · 28 hydrogen bonds · protein-protein
- B–G · 1437 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1128 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6L35 · PSI-LHCI Supercomplex from Physcometrella patens · the same entry in another collection · chain 5 against 5, 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 Q8MFA3
- Every structure of UniProt Q8MFA2
- Every structure of UniProt Q6YXQ2
- Every structure of UniProt A9SRC8
- Every structure of UniProt A0A2K1IKE2
- Every structure of UniProt A0A2K1J0L9
- Every structure of UniProt A9SJ10
- Every structure of UniProt A9SL09
- Every structure of UniProt Q6YXR3
- Every structure of UniProt Q6YXM2
- Every structure of UniProt A9SFV4
- Every structure of UniProt A9S7M7
- Every structure of UniProt Q6YXK4
- Every structure of UniProt A0A2K1K0C7
- Every structure of UniProt A9T399
- Every structure of UniProt A9TEM8
- Every structure of UniProt A0A2K1KN29
- Elsewhere: RCSB PDB 6L35 · PDBe 6L35 · UniProt Q8MFA3 · UniProt Q8MFA2 · UniProt Q6YXQ2 · UniProt A9SRC8 · UniProt A0A2K1IKE2 · UniProt A0A2K1J0L9 · UniProt A9SJ10 · UniProt A9SL09 · UniProt Q6YXR3 · UniProt Q6YXM2 · UniProt A9SFV4 · UniProt A9S7M7 · UniProt Q6YXK4 · UniProt A0A2K1K0C7 · UniProt A9T399 · UniProt A9TEM8 · UniProt A0A2K1KN29
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