MolNFT v1 · #160541 · protein
Structure of photosystem I acclimated to far-red light
6PNJ · Photosystem I P700 chlorophyll a apoprotein A1: “Structure of photosystem I acclimated to far-red light”. Electron microscopy, 9 ligands (CLA, BCR, F6C), 20 pockets (best druggability 0.84). MolNFT v1 #160541 on GenesisL1: 3D…
- PDB
- 6PNJ
- Type
- protein
- Length
- 6,708 residues
- Chains
- 36
- 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
- G6FME9, A0A2N6KXB6, G6FW50, G6FW99, G6FQU3, G6FMD3, A0A2N6MR25, G6FMD2, G6FV28, A0A2N6M3Z9, G6FWT6, G6FSH2
- Ligands
- CLA, BCR, F6C, LMG, SF4, PQN, LHG, CL0, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 12 distinct chains · 47% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, a | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 747 | 53% helix, 4% strand | G6FME9 |
| B, H, b | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 738 | 54% helix, 1% strand | A0A2N6KXB6 |
| C, N, c | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 10% helix, 20% strand | G6FW50 |
| D, O, d | Photosystem I protein psad | protein | 139 | 14% helix, 22% strand | G6FW99 |
| E, P, e | Photosystem I reaction center subunit IV | protein | 62 | 0% helix, 32% strand | G6FQU3 |
| F, Q, f | Photosystem I reaction center protein psaf subunit III | protein | 135 | 41% helix, 5% strand | G6FMD3 |
| I, R, i | Photosystem I subunit VIII | protein | 42 | 52% helix, 2% strand | A0A2N6MR25 |
| J, S, j | Photosystem I reaction centre subunit IX / psaj | protein | 43 | 35% helix, 0% strand | G6FMD2 |
| K, T, k | Photosystem I reaction center subunit psak | protein | 34 | 62% helix, 0% strand | G6FV28 |
| L, U, l | Photosystem I reaction center protein subunit XI | protein | 156 | 49% helix, 4% strand | A0A2N6M3Z9 |
| M, V, m | Photosystem I reaction center subunit XII | protein | 31 | 71% helix, 0% strand | G6FWT6 |
| W, X, x | Photosystem one psax | protein | 29 | 52% helix, 0% strand | G6FSH2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 252 copies · chains A, B, I, F, J, K, L, M, U, X, G, H, R, Q, S, T, V, l, W, i, a, b, f, j, k, m, x
- BCR · Beta-carotene · ligand · 63 copies · chains A, K, B, J, F, G, T, H, S, Q, I, L, U, M, R, l, V, a, k, b, j, f, i, m
- F6C · Chlorophyll F · ligand · 12 copies · chains A, K, B, F, J, L, G, T, H, Q, S, U, a, k, b, f, j, l
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains A, L, B, G, U, H, I, M, i, R, V, l, a, b, m
- SF4 · Iron/sulfur cluster · ligand · 9 copies · chains A, B, C, G, H, N, a, b, c
- PQN · Phylloquinone · ligand · 6 copies · chains A, J, B, G, S, H, a, j, b
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains A, B, X, G, H, W, a, b, x
- CL0 · Chlorophyll A isomer · ligand · 3 copies · chains A, B, G, H, a, b
- CA · Calcium ion · metal · 3 copies · chains A, L, U, G, l, a
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, m, G, M, V, a
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 | 587 | 0.84 | 0.89 | 63 | BCR |
| 2 | 841 | 0.84 | 0.86 | 82 | CL0, CLA |
| 3 | 828 | 0.84 | 0.85 | 82 | CL0, CLA |
| 4 | 674 | 0.83 | 0.86 | 63 | CL0, CLA |
| 5 | 961 | 0.78 | 0.80 | 66 | LMG |
Interfaces
96 interfaces between chains.
- A–B · 3573 Ų buried · 36 hydrogen bonds · protein-protein
- a–b · 3567 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 3560 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1708 Ų buried · 29 hydrogen bonds · protein-protein
- N–O · 1706 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6PNJ · Structure of Photosystem I Acclimated to Far-red Light · 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 G6FME9
- Every structure of UniProt A0A2N6KXB6
- Every structure of UniProt G6FW50
- Every structure of UniProt G6FW99
- Every structure of UniProt G6FQU3
- Every structure of UniProt G6FMD3
- Every structure of UniProt A0A2N6MR25
- Every structure of UniProt G6FMD2
- Every structure of UniProt G6FV28
- Every structure of UniProt A0A2N6M3Z9
- Every structure of UniProt G6FWT6
- Every structure of UniProt G6FSH2
- Elsewhere: RCSB PDB 6PNJ · PDBe 6PNJ · UniProt G6FME9 · UniProt A0A2N6KXB6 · UniProt G6FW50 · UniProt G6FW99 · UniProt G6FQU3 · UniProt G6FMD3 · UniProt A0A2N6MR25 · UniProt G6FMD2 · UniProt G6FV28 · UniProt A0A2N6M3Z9 · UniProt G6FWT6 · UniProt G6FSH2
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