Research workbench
Room temperature xfel crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I
Analyse Room temperature xfel crystallography reveals asymmetry in the vicinity of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M76
- Type
- protein
- Length
- 2,244 residues
- Chains
- 12
- Method
- x-ray diffraction
- 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
- P0A405, P0A407, P0A415, P0A420, P0A423, P0A401, P0A427, P0A429, P0A425, Q8DGB4, P0A403, Q8DKP6
- Ligands
- CLA, BCR, LMG, LHG, SF4, PQN, CL0, DGD, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 12 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 740 | 60% helix, 4% strand | P0A405 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 739 | 60% helix, 3% strand | P0A407 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 20% helix, 21% strand | P0A415 |
| D | Photosystem I reaction center subunit II | protein | 138 | 20% helix, 27% strand | P0A420 |
| E | Photosystem I reaction center subunit IV | protein | 69 | 0% helix, 29% strand | P0A423 |
| F | Photosystem I reaction center subunit III | protein | 141 | 51% helix, 5% strand | P0A401 |
| I | Photosystem I reaction center subunit VIII | protein | 38 | 68% helix, 0% strand | P0A427 |
| J | Photosystem I reaction center subunit IX | protein | 41 | 68% helix, 0% strand | P0A429 |
| K | Photosystem I reaction center subunit psak | protein | 47 | 45% helix, 0% strand | P0A425 |
| L | Photosystem I reaction center subunit XI | protein | 151 | 63% helix, 4% strand | Q8DGB4 |
| M | Photosystem I reaction center subunit XII | protein | 31 | 77% helix, 0% strand | P0A403 |
| X | Photosystem I 4.8K protein | protein | 29 | 69% helix, 0% strand | Q8DKP6 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 95 copies · chains A, B, F, J, K, L, M, I, X
- BCR · Beta-carotene · ligand · 22 copies · chains A, B, F, J, I, K, L, M
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 4 copies · chains A, L, B, I
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 4 copies · chains A, E, B, X, I, M
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains L
- CA · Calcium ion · metal · 2 copies · chains B, A, L
- LMT · Dodecyl-beta-D-maltoside · additive · chains L
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 | 776 | 0.79 | 0.82 | 68 | LMG |
| 2 | 461 | 0.79 | 0.86 | 43 | CL0, CLA |
| 3 | 401 | 0.78 | 0.86 | 41 | CLA |
| 4 | 763 | 0.73 | 0.78 | 81 | CLA, LHG |
| 5 | 848 | 0.72 | 0.76 | 88 | CLA, BCR |
Interfaces
27 interfaces between chains.
- A–B · 3486 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 1577 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 1118 Ų buried · 20 hydrogen bonds · protein-protein
- B–M · 1023 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 902 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7M76 · Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two… · the same entry in another collection · chain X against X, 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 P0A405
- Every structure of UniProt P0A407
- Every structure of UniProt P0A415
- Every structure of UniProt P0A420
- Every structure of UniProt P0A423
- Every structure of UniProt P0A401
- Every structure of UniProt P0A427
- Every structure of UniProt P0A429
- Every structure of UniProt P0A425
- Every structure of UniProt Q8DGB4
- Every structure of UniProt P0A403
- Every structure of UniProt Q8DKP6
- Elsewhere: RCSB PDB 7M76 · PDBe 7M76 · UniProt P0A405 · UniProt P0A407 · UniProt P0A415 · UniProt P0A420 · UniProt P0A423 · UniProt P0A401 · UniProt P0A427 · UniProt P0A429 · UniProt P0A425 · UniProt Q8DGB4 · UniProt P0A403 · UniProt Q8DKP6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.