Research workbench
Membrane protein megahertz crystallography at the european xfel, photosystem I xfel at 2.9 a
Analyse Membrane protein megahertz crystallography at the european xfel, photosystem I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PGK
- Type
- protein
- Length
- 6,720 residues
- Chains
- 36
- 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
- P0A405, P0A407, P0A415, P0A420, P0A423, P0A401, P0A427, P0A429, P0A425, Q8DGB4, P0A403, Q8DKP6
- Ligands
- CLA, BCR, SF4, LHG, PQN, CL0, LMG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 12 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, Y | Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12) | protein | 741 | 56% helix, 3% strand | P0A405 |
| B, H, Z | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) | protein | 739 | 58% helix, 3% strand | P0A407 |
| C, N, a | Photosystem I iron-sulfur center (EC 1.97.1.12) | protein | 80 | 9% helix, 21% strand | P0A415 |
| D, O, b | Photosystem I reaction center subunit II | protein | 138 | 17% helix, 26% strand | P0A420 |
| E, P, c | Photosystem I reaction center subunit IV | protein | 69 | 0% helix, 29% strand | P0A423 |
| F, Q, d | Photosystem I reaction center subunit III | protein | 141 | 53% helix, 5% strand | P0A401 |
| I, R, e | Photosystem I reaction center subunit VIII | protein | 38 | 63% helix, 3% strand | P0A427 |
| J, S, f | Photosystem I reaction center subunit IX | protein | 41 | 68% helix, 2% strand | P0A429 |
| K, T, g | Photosystem I reaction center subunit psak | protein | 46 | 41% helix, 0% strand | P0A425 |
| L, U, h | Photosystem I reaction center subunit XI | protein | 151 | 56% helix, 2% strand | Q8DGB4 |
| M, V, i | Photosystem I reaction center subunit XII | protein | 30 | 73% helix, 0% strand | P0A403 |
| W, X, j | Photosystem I 4.8K protein | protein | 26 | 85% helix, 0% strand | Q8DKP6 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 282 copies · chains A, B, F, J, K, L, D, I, Z, i, M, X, G, H, S, T, h, Q, R, V, U, g, W, e, Y, d, f, j
- BCR · Beta-carotene · ligand · 66 copies · chains A, B, F, J, G, H, S, Q, I, K, L, U, M, R, h, T, Z, e, Y, V, g, d, f, i
- SF4 · Iron/sulfur cluster · ligand · 9 copies · chains A, B, C, G, H, N, Y, Z, a
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 9 copies · chains A, E, B, X, G, P, H, W, Y, c, Z, j
- PQN · Phylloquinone · ligand · 6 copies · chains A, J, B, G, S, H, Y, f, Z
- CL0 · Chlorophyll A isomer · ligand · 3 copies · chains A, B, G, H, Y, Z
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 3 copies · chains B, H, Z
- CA · Calcium ion · metal · 3 copies · chains A, L, h, U, Y, G
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 | 990 | 0.86 | 0.86 | 89 | CL0, CLA |
| 2 | 977 | 0.86 | 0.86 | 89 | CL0, CLA |
| 3 | 903 | 0.85 | 0.86 | 88 | CL0, CLA |
| 4 | 931 | 0.84 | 0.85 | 93 | BCR, CLA |
| 5 | 857 | 0.81 | 0.83 | 64 | LMG |
Interfaces
97 interfaces between chains.
- A–B · 3531 Ų buried · 49 hydrogen bonds · protein-protein
- Y–Z · 3494 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 3480 Ų buried · 40 hydrogen bonds · protein-protein
- a–b · 1639 Ų buried · 31 hydrogen bonds · protein-protein
- N–O · 1616 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6PGK · Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I XFEL at… · the same entry in another collection · chain D against D, 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 P0A405
- Every structure of UniProt P0A407
- Every structure of UniProt P0A415
- Every structure of UniProt P0A420
- Every structure of UniProt P0A423
- Every structure of UniProt P0A401
- Every structure of UniProt P0A427
- Every structure of UniProt P0A429
- Every structure of UniProt P0A425
- Every structure of UniProt Q8DGB4
- Every structure of UniProt P0A403
- Every structure of UniProt Q8DKP6
- Elsewhere: RCSB PDB 6PGK · PDBe 6PGK · UniProt P0A405 · UniProt P0A407 · UniProt P0A415 · UniProt P0A420 · UniProt P0A423 · UniProt P0A401 · UniProt P0A427 · UniProt P0A429 · UniProt P0A425 · UniProt Q8DGB4 · UniProt P0A403 · UniProt Q8DKP6
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