Research workbench
Red alga C.MEROLAE photosystem I
Analyse Red alga C.MEROLAE photosystem I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BLZ
- Type
- protein
- Length
- 2,817 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similar to light harvesting protein; Similar to chlorophyll A/B-binding protein, CP24…
- EC
- 1.97.1.12
- UniProt
- M1VKK5, M1UU36, Q85FY7, Q85FY6, Q85G47, Q85FY0, Q85FZ1, A0A5P9RU83, Q85FQ6, A0A5P9RTH6, Q85G51, Q85FP8, Q85G73, M1VFJ4
- Ligands
- CLA, BCR, C7Z, LHG, RRX, PTY, ERG, SF4, 3PH, DGD, PGT, DGA, LMU, PQN, CL0, T7X…
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 15 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Similar to light harvesting protein | protein | 173 | 46% helix, 0% strand | M1VKK5 |
| 2 | Similar to chlorophyll A/B-binding protein, CP24 | protein | 179 | 53% helix, 0% strand | M1UU36 |
| 3 | LHCR3 | protein | 174 | 56% helix, 0% strand | — |
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 743 | 61% helix, 5% strand | Q85FY7 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 731 | 61% helix, 2% strand | Q85FY6 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 21% strand | Q85G47 |
| D | Photosystem I P700 chlorophyll a apoprotein A2 | protein | 138 | 18% helix, 26% strand | Q85FY0 |
| E | Photosystem I iron-sulfur center subunit VII | protein | 61 | 5% helix, 34% strand | Q85FZ1 |
| F | Psi-F | protein | 155 | 59% helix, 5% strand | A0A5P9RU83 |
| I | Photosystem I reaction center subunit VIII | protein | 31 | 87% helix, 0% strand | Q85FQ6 |
| J | Photosystem I reaction center subunit IX | protein | 38 | 71% helix, 3% strand | A0A5P9RTH6 |
| K | Psi-K | protein | 54 | 85% helix, 0% strand | Q85G51 |
| L | Photosystem I reaction center subunit XI | protein | 136 | 62% helix, 4% strand | Q85FP8 |
| M | Photosystem I reaction center subunit XII | protein | 27 | 89% helix, 0% strand | Q85G73 |
| O | Psao | protein | 97 | 58% helix, 5% strand | M1VFJ4 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 132 copies · chains 1, 2, F, J, 3, A, K, B, O, L, I, M
- BCR · Beta-carotene · ligand · 22 copies · chains 2, 3, A, O, K, B, I, M, F, J, L
- C7Z · (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E}, 9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol · ligand · 13 copies · chains 1, 2, 3, A, J
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains 1, 2, 3, A, B
- RRX · (3R)-beta,beta-caroten-3-ol · ligand · 5 copies · chains 1, 2, A, B, J, 3, K
- PTY · Phosphatidylethanolamine · ligand · 4 copies · chains 3, A, O, L
- ERG · Ergosterol · ligand · 3 copies · chains 1, 2, J, 3, A
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 3 copies · chains 2, A, J, B, 1, F
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 3 copies · chains B, C, I, L, M
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 2 copies · chains 2, 3, B
- DGA · Diacyl glycerol · ligand · 2 copies · chains 2, A, 1, J
- LMU · Dodecyl-alpha-D-maltoside · ligand · 2 copies · chains 2, 3, A, J
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- T7X · Phosphatidylinositol · ligand · chains A, L
- CA · Calcium ion · metal · 2 copies · chains B
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 | 793 | 0.84 | 0.86 | 72 | CL0, CLA |
| 2 | 899 | 0.78 | 0.81 | 77 | CLA, DGD |
| 3 | 331 | 0.76 | 0.86 | 40 | CLA |
| 4 | 1181 | 0.71 | 0.75 | 105 | CLA, LHG |
| 5 | 679 | 0.71 | 0.77 | 60 | CLA |
Interfaces
33 interfaces between chains.
- A–B · 3520 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1600 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 1086 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1073 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 879 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7BLZ · Red alga C.merolae Photosystem I · the same entry in another collection · chain O against O, 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 M1VKK5
- Every structure of UniProt M1UU36
- Every structure of UniProt Q85FY7
- Every structure of UniProt Q85FY6
- Every structure of UniProt Q85G47
- Every structure of UniProt Q85FY0
- Every structure of UniProt Q85FZ1
- Every structure of UniProt A0A5P9RU83
- Every structure of UniProt Q85FQ6
- Every structure of UniProt A0A5P9RTH6
- Every structure of UniProt Q85G51
- Every structure of UniProt Q85FP8
- Every structure of UniProt Q85G73
- Every structure of UniProt M1VFJ4
- Elsewhere: RCSB PDB 7BLZ · PDBe 7BLZ · UniProt M1VKK5 · UniProt M1UU36 · UniProt Q85FY7 · UniProt Q85FY6 · UniProt Q85G47 · UniProt Q85FY0 · UniProt Q85FZ1 · UniProt A0A5P9RU83 · UniProt Q85FQ6 · UniProt A0A5P9RTH6 · UniProt Q85G51 · UniProt Q85FP8 · UniProt Q85G73 · UniProt M1VFJ4
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