MolNFT v1 · #151521 · protein
Monomeric cyanobacterial photosystem I
6HQB · Photosystem I P700 chlorophyll a apoprotein A1: “Monomeric cyanobacterial photosystem I”. X-ray diffraction, 13 ligands (CLA, BCR, LHG), 20 pockets (best druggability 0.86). MolNFT v1 #151521 on GenesisL1: 3D structure, binding…
- PDB
- 6HQB
- Type
- protein
- Length
- 2,232 residues
- Chains
- 11
- 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
- P29254, P29255, P32422, P19569, P12975, P29256, Q55330, Q55329, P74564, P37277, P72986
- Ligands
- CLA, BCR, LHG, SF4, PQN, ECH, LMG, SQD, C7Z, 45D, EQ3, CA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 11 distinct chains · 52% 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 | 750 | 59% helix, 4% strand | P29254 |
| B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 731 | 60% helix, 2% strand | P29255 |
| C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 15% helix, 20% strand | P32422 |
| D | Photosystem I reaction center subunit II | protein | 141 | 16% helix, 26% strand | P19569 |
| E | Photosystem I reaction center subunit IV | protein | 69 | 4% helix, 30% strand | P12975 |
| F | Photosystem I reaction center subunit III | protein | 143 | 50% helix, 6% strand | P29256 |
| I | Photosystem I reaction center subunit VIII | protein | 40 | 65% helix, 0% strand | Q55330 |
| J | Photosystem I reaction center subunit IX | protein | 40 | 70% helix, 3% strand | Q55329 |
| K | Photosystem I reaction center subunit psak 2 | protein | 70 | 60% helix, 0% strand | P74564 |
| L | Photosystem I reaction center subunit XI | protein | 137 | 45% helix, 0% strand | P37277 |
| M | Photosystem I reaction center subunit XII | protein | 31 | 81% helix, 0% strand | P72986 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 93 copies · chains A, B, J, K, L, F, M, I
- BCR · Beta-carotene · ligand · 14 copies · chains A, K, J, B, F, I
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 4 copies · chains A, E, B
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- ECH · beta,beta-caroten-4-one · ligand · 2 copies · chains B, M
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 2 copies · chains B
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 2 copies · chains B, A, F
- C7Z · (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E}, 9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol · ligand · 2 copies · chains A, B, F, J
- 45D · beta,beta-carotene-4,4'-dione · ligand · chains A, B
- EQ3 · (3'R)-3'-hydroxy-beta,beta-caroten-4-one · ligand · chains B, I, L
- CA · Calcium ion · metal · 2 copies · chains B, A, L
- CL · Chloride ion · ion · chains A, B
- LMT · Dodecyl-beta-D-maltoside · additive · chains F, J
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 | 1025 | 0.86 | 0.86 | 100 | CLA |
| 2 | 829 | 0.81 | 0.83 | 66 | LMG |
| 3 | 66 | 0.74 | 0.98 | 19 | SF4 |
| 4 | 79 | 0.73 | 0.97 | 22 | empty |
| 5 | 752 | 0.72 | 0.78 | 81 | CLA, LHG |
Interfaces
23 interfaces between chains.
- A–B · 3522 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1609 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1310 Ų buried · 16 hydrogen bonds · protein-protein
- B–M · 1035 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 983 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
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 P29254
- Every structure of UniProt P29255
- Every structure of UniProt P32422
- Every structure of UniProt P19569
- Every structure of UniProt P12975
- Every structure of UniProt P29256
- Every structure of UniProt Q55330
- Every structure of UniProt Q55329
- Every structure of UniProt P74564
- Every structure of UniProt P37277
- Every structure of UniProt P72986
- Elsewhere: RCSB PDB 6HQB · PDBe 6HQB · UniProt P29254 · UniProt P29255 · UniProt P32422 · UniProt P19569 · UniProt P12975 · UniProt P29256 · UniProt Q55330 · UniProt Q55329 · UniProt P74564 · UniProt P37277 · UniProt P72986
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