Research workbench
Crystal structure of a virus like photosystem I from the cyanobacterium synechocystis pcc 6803
Analyse Crystal structure of a virus like photosystem I from the cyanobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L6V
- Type
- protein
- Length
- 6,534 residues
- Chains
- 30
- 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
- L8AHT3, L8AIC0, L8AST2, L8AFM8, L8ASH8, L8AII8, Q55329, L8APN7, L8ADF9, L8AP84, L8APJ0
- Ligands
- CLA, BCR, SF4, LHG, PQN, LMG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 10 distinct chains · 54% 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 | 739 | 59% helix, 5% strand | L8AHT3 |
| B, b, 2 | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 728 | 59% helix, 3% strand | L8AIC0 |
| C, c, 3 | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 10% helix, 20% strand | L8AST2 |
| D, d, 4 | Photosystem I subunit II (EC 1.97.1.12) | protein | 138 | 14% helix, 24% strand | L8AFM8 |
| E, e, 5 | Photosystem I reaction center subunit IV (EC 1.97.1.12) | protein | 68 | 4% helix, 34% strand | L8ASH8 |
| F, f, 6 | Fusion protein of photosystem I subunit III and subunit IX (EC 1.97.1.12) | protein | 125 | 56% helix, 0% strand | L8AII8, Q55329 |
| L, l, 8 | Photosystem I reaction center subunit XI (EC 1.97.1.12) | protein | 151 | 66% helix, 5% strand | L8APN7 |
| M, m, 7 | Photosystem I reaction center subunit XII (EC 1.97.1.12) | protein | 31 | 84% helix, 0% strand | L8ADF9 |
| i, 9, I | Photosystem I subunit III (EC 1.97.1.12) | protein | 38 | 66% helix, 0% strand | L8AP84 |
| K, k, 0 | Photosystem I reaction center subunit VIII (EC 1.97.1.12) | protein | 80 | 58% helix, 0% strand | L8APJ0 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 273 copies · chains A, B, F, K, L, I, M, a, b, f, k, l, i, m, 1, 2, 6, 0, 8, 9, 7
- BCR · Beta-carotene · ligand · 57 copies · chains A, K, B, F, I, L, M, a, k, b, f, i, l, m, 1, 0, 2, 6, 9, 8, 7
- SF4 · Iron/sulfur cluster · ligand · 9 copies · chains A, B, C, a, b, c, 1, 2, 3
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 9 copies · chains A, E, B, a, e, b, 1, 5, 2
- PQN · Phylloquinone · ligand · 6 copies · chains A, B, a, f, b, 1, 6, 2
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 3 copies · chains B, b, 2
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 | 864 | 0.84 | 0.86 | 86 | CLA |
| 2 | 894 | 0.81 | 0.83 | 68 | LMG |
| 3 | 1001 | 0.80 | 0.81 | 70 | LMG, CLA |
| 4 | 1192 | 0.80 | 0.81 | 89 | LMG, CLA |
| 5 | 450 | 0.78 | 0.86 | 47 | CLA |
Interfaces
65 interfaces between chains.
- A–B · 3592 Ų buried · 39 hydrogen bonds · protein-protein
- 1–2 · 3567 Ų buried · 36 hydrogen bonds · protein-protein
- a–b · 3556 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1614 Ų buried · 21 hydrogen bonds · protein-protein
- c–d · 1602 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent (covalent ligand).
Compared structures
- 4L6V · Crystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC… · the same entry in another collection · chain A against A, 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 L8AHT3
- Every structure of UniProt L8AIC0
- Every structure of UniProt L8AST2
- Every structure of UniProt L8AFM8
- Every structure of UniProt L8ASH8
- Every structure of UniProt L8AII8
- Every structure of UniProt Q55329
- Every structure of UniProt L8APN7
- Every structure of UniProt L8ADF9
- Every structure of UniProt L8AP84
- Every structure of UniProt L8APJ0
- Elsewhere: RCSB PDB 4L6V · PDBe 4L6V · UniProt L8AHT3 · UniProt L8AIC0 · UniProt L8AST2 · UniProt L8AFM8 · UniProt L8ASH8 · UniProt L8AII8 · UniProt Q55329 · UniProt L8APN7 · UniProt L8ADF9 · UniProt L8AP84 · UniProt L8APJ0
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