Research workbench
Cyanidioschyzon merolae photosystem I
Analyse Cyanidioschyzon 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
- 6FOS
- Type
- protein
- Length
- 2,684 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similar to chlorophyll A/B-binding protein, CP24; Similar to light harvesting protein…
- EC
- 1.97.1.12
- UniProt
- M1UU36, M1VKK5, Q85FY7, Q85FY6, Q85G47, Q85FY0, Q85FZ1, Q85FS9, Q85FQ6, Q85FS8, Q85G51, Q85FP8, Q85G73, M1VFJ4
- Ligands
- CLA, BCR, SF4, PQN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 15 distinct chains · 51% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | Similar to chlorophyll A/B-binding protein, CP24 | protein | 144 | 69% helix, 0% strand | M1UU36 |
| 3 | Similar to chlorophyll A/B-binding protein, CP24 | protein | 150 | 35% helix, 0% strand | M1UU36 |
| 4 | Similar to light harvesting protein | protein | 116 | 62% helix, 0% strand | M1VKK5 |
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 740 | 53% helix, 3% strand | Q85FY7 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 724 | 54% helix, 2% strand | Q85FY6 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 20% helix, 18% strand | Q85G47 |
| D | Photosystem I P700 chlorophyll a apoprotein A2 | protein | 124 | 15% helix, 18% strand | Q85FY0 |
| E | Photosystem I iron-sulfur center subunit VII | protein | 69 | 0% helix, 19% strand | Q85FZ1 |
| F | Photosystem I reaction center subunit II | protein | 153 | 63% helix, 0% strand | Q85FS9 |
| I | Photosystem I reaction center subunit VIII | protein | 32 | 75% helix, 0% strand | Q85FQ6 |
| J | Photosystem I reaction center subunit IX | protein | 38 | 66% helix, 0% strand | Q85FS8 |
| K | Photosystem I reaction center subunit X | protein | 47 | 70% helix, 0% strand | Q85G51 |
| L | Photosystem I reaction center subunit XI | protein | 140 | 58% helix, 0% strand | Q85FP8 |
| M | Photosystem I reaction center subunit XII | protein | 29 | 79% helix, 0% strand | Q85G73 |
| O | Psam | protein | 98 | 44% helix, 0% strand | M1VFJ4 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 134 copies · chains 2, 3, 4, K, F, A, B, J, D, L, I, O
- BCR · Beta-carotene · ligand · 8 copies · chains A, B, F, J, I
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, 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 | 1071 | 0.81 | 0.82 | 114 | PQN, SF4, CLA |
| 2 | 1069 | 0.78 | 0.79 | 108 | CLA |
| 3 | 356 | 0.76 | 0.86 | 41 | CLA |
| 4 | 1093 | 0.75 | 0.78 | 96 | CLA |
| 5 | 259 | 0.75 | 0.88 | 32 | empty |
Interfaces
31 interfaces between chains.
- A–B · 3506 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1552 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1199 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 974 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 841 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6FOS · Cyanidioschyzon 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 M1UU36
- Every structure of UniProt M1VKK5
- 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 Q85FS9
- Every structure of UniProt Q85FQ6
- Every structure of UniProt Q85FS8
- Every structure of UniProt Q85G51
- Every structure of UniProt Q85FP8
- Every structure of UniProt Q85G73
- Every structure of UniProt M1VFJ4
- Elsewhere: RCSB PDB 6FOS · PDBe 6FOS · UniProt M1UU36 · UniProt M1VKK5 · UniProt Q85FY7 · UniProt Q85FY6 · UniProt Q85G47 · UniProt Q85FY0 · UniProt Q85FZ1 · UniProt Q85FS9 · UniProt Q85FQ6 · UniProt Q85FS8 · UniProt Q85G51 · UniProt Q85FP8 · UniProt Q85G73 · UniProt M1VFJ4
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