Research workbench
Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light
Analyse Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LX0
- Type
- protein
- Length
- 6,774 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, A0A2N6L446, G6FWT6, G6FSH2
- Ligands
- CLA, BCR, F6C, LMG, SF4, PQN, LHG, CL0, CA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 12 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, a, A | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 751 | 57% helix, 4% strand | G6FME9 |
| H, b, B | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 739 | 58% helix, 3% strand | A0A2N6KXB6 |
| N, c, C | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 16% helix, 21% strand | G6FW50 |
| O, d, D | Photosystem I protein psad | protein | 139 | 12% helix, 26% strand | G6FW99 |
| P, e, E | Photosystem I reaction center subunit IV | protein | 62 | 0% helix, 34% strand | G6FQU3 |
| Q, f, F | Photosystem I reaction center protein psaf subunit III | protein | 135 | 51% helix, 5% strand | G6FMD3 |
| R, i, I | Photosystem I subunit VIII | protein | 42 | 57% helix, 2% strand | A0A2N6MR25 |
| S, j, J | Photosystem I reaction centre subunit IX / psaj | protein | 43 | 56% helix, 0% strand | G6FMD2 |
| T, k, K | Photosystem I reaction center subunit psak | protein | 44 | 50% helix, 0% strand | — |
| U, l, L | Psi subunit V | protein | 163 | 56% helix, 4% strand | A0A2N6L446 |
| V, m, M | Photosystem I reaction center subunit XII | protein | 31 | 74% 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 G, H, R, Q, S, T, U, B, V, W, I, L, a, b, i, f, j, k, l, m, x, A, F, J, K, M, X
- BCR · Beta-carotene · ligand · 60 copies · chains G, T, H, W, S, Q, R, U, l, V, a, k, b, x, j, f, i, L, m, A, K, B, X, J, F, I, M
- F6C · Chlorophyll F · ligand · 15 copies · chains G, H, R, U, l, Q, S, a, b, i, L, f, j, A, B, I, F, J
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains G, U, H, R, V, l, I, a, b, i, m, L, A, B, M
- SF4 · Iron/sulfur cluster · ligand · 9 copies · chains G, H, N, a, b, c, A, B, C
- PQN · Phylloquinone · ligand · 6 copies · chains G, S, H, a, j, b, A, J, B
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains G, H, W, a, b, x, A, B, X
- CL0 · Chlorophyll A isomer · ligand · 3 copies · chains G, H, a, b, A, B
- CA · Calcium ion · metal · 3 copies · chains G, U, a, l, A, L
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains G, M, V, a, m, 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 | 1075 | 0.86 | 0.86 | 99 | CL0, CLA |
| 2 | 1116 | 0.86 | 0.86 | 99 | CL0, CLA |
| 3 | 1095 | 0.85 | 0.86 | 98 | CL0, CLA |
| 4 | 645 | 0.83 | 0.87 | 76 | F6C, BCR |
| 5 | 808 | 0.78 | 0.82 | 63 | LMG |
Interfaces
99 interfaces between chains.
- A–B · 3570 Ų buried · 39 hydrogen bonds · protein-protein
- a–b · 3554 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 3552 Ų buried · 39 hydrogen bonds · protein-protein
- N–O · 1679 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1679 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7LX0 · Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated… · the same entry in another collection · chain N against N, 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 A0A2N6L446
- Every structure of UniProt G6FWT6
- Every structure of UniProt G6FSH2
- Elsewhere: RCSB PDB 7LX0 · PDBe 7LX0 · UniProt G6FME9 · UniProt A0A2N6KXB6 · UniProt G6FW50 · UniProt G6FW99 · UniProt G6FQU3 · UniProt G6FMD3 · UniProt A0A2N6MR25 · UniProt G6FMD2 · UniProt A0A2N6L446 · UniProt G6FWT6 · UniProt G6FSH2
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