Research workbench
Structure of wild-type psi MONOMER2 from cyanophora paradoxa
Analyse Structure of wild-type psi MONOMER2 from cyanophora paradoxa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DR1
- Type
- protein
- Length
- 2,114 residues
- Chains
- 10
- 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
- A0A097PBL3, P48113, P31173, Q9T4W8, P48114, P48115, P48116, P48117, P48185
- Ligands
- CLA, BCR, SF4, PQN, LHG, CL0, LMG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 53% 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 | 739 | 57% helix, 5% strand | A0A097PBL3 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 706 | 62% helix, 3% strand | P48113 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 8% helix, 20% strand | P31173 |
| D | Photosystem I reaction center subunit II, cyanelle | protein | 139 | 12% helix, 13% strand | Q9T4W8 |
| E | Photosystem I reaction center subunit IV | protein | 62 | 5% helix, 32% strand | P48114 |
| F | Photosystem I reaction center subunit III | protein | 161 | 57% helix, 5% strand | P48115 |
| I | Photosystem I reaction center subunit VIII | protein | 30 | 77% helix, 3% strand | P48116 |
| J | Photosystem I reaction center subunit IX | protein | 37 | 68% helix, 3% strand | P48117 |
| L | Photosystem I reaction center subunit XI | protein | 131 | 61% helix, 0% strand | — |
| M | Photosystem I reaction center subunit XII | protein | 29 | 86% helix, 0% strand | P48185 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 80 copies · chains A, B, F, J, L, D, I, M
- BCR · Beta-carotene · ligand · 19 copies · chains A, B, F, J, I, L, M
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains A
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 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 | 910 | 0.85 | 0.86 | 83 | CL0, CLA |
| 2 | 1055 | 0.75 | 0.78 | 111 | CLA, BCR |
| 3 | 900 | 0.75 | 0.78 | 65 | LMG |
| 4 | 802 | 0.74 | 0.79 | 98 | CLA, LHG |
| 5 | 693 | 0.72 | 0.78 | 60 | CLA |
Interfaces
23 interfaces between chains.
- A–B · 3577 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1579 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1167 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 1156 Ų buried · 14 hydrogen bonds · protein-protein
- B–M · 895 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7DR1 · Structure of Wild-type PSI monomer2 from Cyanophora paradoxa · the same entry in another collection · chain M against M, TM-score 1.00
- P48113 · AlphaFold monomer V2.0 prediction for photosystem I P700 chlorophyll a apoprotein A2… · a predicted model of the same protein · chain B against A, TM-score 1.00
- P48114 · AlphaFold monomer V2.0 prediction for photosystem I reaction center subunit IV (P48114) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 A0A097PBL3
- Every structure of UniProt P48113
- Every structure of UniProt P31173
- Every structure of UniProt Q9T4W8
- Every structure of UniProt P48114
- Every structure of UniProt P48115
- Every structure of UniProt P48116
- Every structure of UniProt P48117
- Every structure of UniProt P48185
- Elsewhere: RCSB PDB 7DR1 · PDBe 7DR1 · UniProt A0A097PBL3 · UniProt P48113 · UniProt P31173 · UniProt Q9T4W8 · UniProt P48114 · UniProt P48115 · UniProt P48116 · UniProt P48117 · UniProt P48185
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