Research workbench
Improved model of plant photosystem I
Analyse Improved model of plant photosystem I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LW5
- Type
- protein
- Length
- 3,182 residues
- Chains
- 18
- 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…
- UniProt
- P05310, P05311, P10793, P17227, Q41038, Q32904, Q9SQL2
- Ligands
- CLA, LMU, BCR, SF4, PQN, LMG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 18 distinct chains · 32% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem I P700 chlorophyll a apoprotein A1 | protein | 730 | 38% helix, 1% strand | P05310 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 | protein | 733 | 36% helix, 1% strand | P05311 |
| C | Photosystem I iron-sulfur center | protein | 81 | 0% helix, 0% strand | P10793 |
| D | Putative uncharacterized protein | protein | 138 | 8% helix, 7% strand | — |
| E | Putative uncharacterized protein | protein | 64 | 0% helix, 13% strand | — |
| F | Photosystem I reaction center subunit III, chloroplastic | protein | 154 | 29% helix, 1% strand | — |
| G | Putative uncharacterized protein | protein | 95 | 21% helix, 0% strand | — |
| H | Putative uncharacterized protein | protein | 69 | 19% helix, 0% strand | — |
| I | Photosystem I reaction center subunit VIII | protein | 30 | 47% helix, 0% strand | P17227 |
| J | Photosystem I reaction center subunit IX | protein | 42 | 14% helix, 0% strand | — |
| K | Photosystem I reaction center subunit X psak | protein | 84 | 50% helix, 0% strand | — |
| L | Putative uncharacterized protein | protein | 161 | 34% helix, 1% strand | — |
| N | Photosystem I-N subunit | protein | 85 | 0% helix, 2% strand | — |
| R | Chain R | protein | 53 | 36% helix, 0% strand | — |
| 1 | AT3G54890 | protein | 165 | 41% helix, 0% strand | — |
| 2 | Type II chlorophyll A/B binding protein from photosystem I | protein | 176 | 41% helix, 0% strand | Q41038 |
| 3 | Chlorophyll a-B binding protein 3, chloroplastic | protein | 156 | 28% helix, 0% strand | Q32904 |
| 4 | Chlorophyll a-B binding protein P4, chloroplastic | protein | 166 | 39% helix, 0% strand | Q9SQL2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 174 copies · chains A, J, B, K, L, F, I, G, H, R, 1, 2, 3, 4
- LMU · Dodecyl-alpha-D-maltoside · ligand · 53 copies · chains A, R, B, D, F, G, K, H, L, N, 2, 4
- BCR · Beta-carotene · ligand · 19 copies · chains A, B, G, I, L, F, J, 3
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, B
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · chains B, C
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 | 835 | 0.84 | 0.86 | 91 | SF4 |
| 2 | 1072 | 0.82 | 0.83 | 137 | empty |
| 3 | 618 | 0.82 | 0.86 | 68 | CLA |
| 4 | 530 | 0.79 | 0.86 | 68 | SF4 |
| 5 | 380 | 0.77 | 0.86 | 47 | CLA |
Interfaces
40 interfaces between chains.
- A–B · 3510 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1310 Ų buried · 14 hydrogen bonds · protein-protein
- B–G · 1132 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 972 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 850 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 covalent, 2 isopeptide (covalent ligand, isopeptide).
Compared structures
- 3LW5 · Improved model of plant photosystem I · the same entry in another collection · chain 4 against 4, 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 P05310
- Every structure of UniProt P05311
- Every structure of UniProt P10793
- Every structure of UniProt P17227
- Every structure of UniProt Q41038
- Every structure of UniProt Q32904
- Every structure of UniProt Q9SQL2
- Elsewhere: RCSB PDB 3LW5 · PDBe 3LW5 · UniProt P05310 · UniProt P05311 · UniProt P10793 · UniProt P17227 · UniProt Q41038 · UniProt Q32904 · UniProt Q9SQL2
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