Research workbench
Trimeric photosystem I from the high-light tolerant cyanobacteria cyanobacterium aponinum
Analyse Trimeric photosystem I from the high-light tolerant cyanobacteria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VPV
- Type
- protein
- Length
- 6,753 residues
- Chains
- 33
- 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
- A0A2G3P9X3, K9Z2J7, A0A2G3PD04, A0A2G3PAQ0, A0A2G3PEU8, A0A2G3PEV5, K9Z9J3, A0A2G3PEV6, A0A2G3P6W6, A0A2G3P7D5, A0A2G3PA81
- Ligands
- CLA, BCR, SF4, PQN, LHG, CL0, LMG, SQD
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a, 1 | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 741 | 59% helix, 5% strand | A0A2G3P9X3 |
| B, b, 2 | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 737 | 57% helix, 2% strand | K9Z2J7 |
| C, c, 3 | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 15% helix, 20% strand | A0A2G3PD04 |
| D, d, 4 | Photosystem I reaction center subunit II | protein | 139 | 12% helix, 26% strand | A0A2G3PAQ0 |
| E, e, 5 | Photosystem I reaction center subunit IV | protein | 68 | 0% helix, 32% strand | A0A2G3PEU8 |
| F, f, 6 | Psi-F | protein | 141 | 47% helix, 6% strand | A0A2G3PEV5 |
| I, i, 7 | Photosystem I reaction center subunit VIII | protein | 38 | 66% helix, 3% strand | K9Z9J3 |
| J, j, 8 | Photosystem I reaction center subunit IX | protein | 39 | 72% helix, 3% strand | A0A2G3PEV6 |
| K, k, 9 | Photosystem I reaction center subunit psak | protein | 78 | 59% helix, 0% strand | A0A2G3P6W6 |
| L, l, 0 | Photosystem I reaction center subunit XI | protein | 160 | 45% helix, 2% strand | A0A2G3P7D5 |
| M, m, z | Photosystem I reaction center subunit XII | protein | 30 | 87% helix, 0% strand | A0A2G3PA81 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 285 copies · chains A, B, J, K, L, I, b, F, m, M, 0, 9, i, l, a, j, k, 2, f, z, 7, 1, 8, 6
- BCR · Beta-carotene · ligand · 69 copies · chains A, B, F, J, I, K, L, 0, M, a, b, f, j, i, k, l, m, 1, 2, 6, 8, 7, 9, z
- SF4 · Iron/sulfur cluster · ligand · 9 copies · chains A, B, C, a, b, c, 1, 2, 3
- PQN · Phylloquinone · ligand · 6 copies · chains A, J, B, a, j, b, 1, 8, 2
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains A, E, a, e, 1, 5
- CL0 · Chlorophyll A isomer · ligand · 3 copies · chains A, B, a, b, 1, 2
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 3 copies · chains B, b, 2
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 3 copies · chains B, I, L, 0, b, i, l, 2, 7
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 | 1134 | 0.86 | 0.86 | 100 | CL0, CLA |
| 2 | 955 | 0.86 | 0.86 | 78 | CL0, CLA |
| 3 | 739 | 0.83 | 0.86 | 74 | CL0, CLA |
| 4 | 1133 | 0.82 | 0.82 | 124 | CLA, BCR |
| 5 | 964 | 0.81 | 0.82 | 91 | CLA, LMG |
Interfaces
87 interfaces between chains.
- a–b · 3507 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 3507 Ų buried · 37 hydrogen bonds · protein-protein
- 1–2 · 3506 Ų buried · 38 hydrogen bonds · protein-protein
- 3–4 · 1649 Ų buried · 17 hydrogen bonds · protein-protein
- c–d · 1644 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6VPV · Trimeric Photosystem I from the High-Light Tolerant Cyanobacteria Cyanobacterium Aponinum · the same entry in another collection · chain B against B, 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 A0A2G3P9X3
- Every structure of UniProt K9Z2J7
- Every structure of UniProt A0A2G3PD04
- Every structure of UniProt A0A2G3PAQ0
- Every structure of UniProt A0A2G3PEU8
- Every structure of UniProt A0A2G3PEV5
- Every structure of UniProt K9Z9J3
- Every structure of UniProt A0A2G3PEV6
- Every structure of UniProt A0A2G3P6W6
- Every structure of UniProt A0A2G3P7D5
- Every structure of UniProt A0A2G3PA81
- Elsewhere: RCSB PDB 6VPV · PDBe 6VPV · UniProt A0A2G3P9X3 · UniProt K9Z2J7 · UniProt A0A2G3PD04 · UniProt A0A2G3PAQ0 · UniProt A0A2G3PEU8 · UniProt A0A2G3PEV5 · UniProt K9Z9J3 · UniProt A0A2G3PEV6 · UniProt A0A2G3P6W6 · UniProt A0A2G3P7D5 · UniProt A0A2G3PA81
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