MolNFT v1 · #91392 · protein
Fs X-ray diffraction of photosystem II
4FBY · Photosystem Q(B) protein 1: “Fs X-ray diffraction of photosystem II”. X-ray diffraction, 14 ligands (CLA, BCR, LMG), 20 pockets (best druggability 0.87). MolNFT v1 #91392 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4FBY
- Type
- protein
- Length
- 5,270 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem Q(B) protein 1; Photosystem II core light harvesting protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, Q8DHA7, P0A431, Q8DIQ0, Q9F1L5, P0A386, Q8DJI1, Q9F1R6, Q8DHJ2
- Ligands
- CLA, BCR, LMG, DGD, SQD, PL9, PHO, LHG, HEM, OEC, BCT, FE2, CA, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 20 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Photosystem Q(B) protein 1 (EC 1.10.3.9) | protein | 335 | 59% helix, 4% strand | P0A444 |
| B, N | Photosystem II core light harvesting protein | protein | 490 | 49% helix, 11% strand | Q8DIQ1 |
| C, P | Photosystem II CP43 protein | protein | 447 | 55% helix, 4% strand | Q8DIF8 |
| D, Q | Photosystem II D2 protein (EC 1.10.3.9) | protein | 340 | 62% helix, 3% strand | Q8CM25 |
| E, R | Cytochrome B559 subunit alpha | protein | 82 | 54% helix, 0% strand | Q8DIP0 |
| F, S | Cytochrome B559 subunit beta | protein | 35 | 66% helix, 0% strand | Q8DIN9 |
| H, W | Photosystem II reaction center protein H | protein | 65 | 43% helix, 5% strand | Q8DJ43 |
| I, a | Photosystem II reaction center protein I | protein | 35 | 66% helix, 0% strand | Q8DJZ6 |
| J, b | Photosystem II reaction center protein J | protein | 34 | 65% helix, 0% strand | P59087 |
| K, c | Photosystem II reaction center protein K | protein | 37 | 76% helix, 0% strand | Q9F1K9 |
| L, d | Photosystem II reaction center protein L | protein | 37 | 62% helix, 3% strand | Q8DIN8 |
| M, e | Photosystem II reaction center protein M | protein | 34 | 71% helix, 0% strand | Q8DHA7 |
| O, f | Photosystem II manganese-stabilizing polypeptide | protein | 243 | 4% helix, 45% strand | P0A431 |
| T, g | Photosystem II reaction center protein T | protein | 32 | 66% helix, 0% strand | Q8DIQ0 |
| U, h | Photosystem II 12 kda extrinsic protein | protein | 97 | 48% helix, 6% strand | Q9F1L5 |
| V, i | Cytochrome C-550 | protein | 137 | 45% helix, 6% strand | P0A386 |
| y, m | Photosystem II reaction center protein YCF12 | protein | 28 | 71% helix, 0% strand | Q8DJI1 |
| X, j | Photosystem II reaction center protein X | protein | 37 | 76% helix, 0% strand | Q9F1R6 |
| Y, k | Photosystem II reaction center protein Y | protein | 28 | 75% helix, 0% strand | — |
| Z, l | Photosystem II reaction center protein Z | protein | 62 | 85% helix, 0% strand | Q8DHJ2 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, L, F, I, B, H, M, e, g, C, K, y, Z, X, G, Q, d, S, a, N, W, P, c, m, l, j
- BCR · Beta-carotene · ligand · 24 copies · chains B, M, g, C, K, Z, I, D, F, J, H, X, A, N, y, T, e, P, c, l, a, Q, S, b, W, j, G, m
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 22 copies · chains A, B, D, L, M, C, J, K, y, Z, F, T, O, N, E, I, d, e, G, Q, P, b, c, m, l, f, g, S, R, a
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 14 copies · chains A, C, I, O, B, D, H, G, J, V, E, F, P, a, f, N, b, Q, i, R, S, W
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 10 copies · chains A, C, D, K, I, T, N, B, H, X, L, d, e, g, E, F, G, a, P, Q, c, M, W, j, R, S
- PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · 6 copies · chains A, D, F, L, T, E, J, G, Q, S, d, g, R, b
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, G, Q
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 4 copies · chains A, C, D, K, G, P, Q, c
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F, Y, C, V, R, S, k, P, i
- OEC · Oxygen evolving system · ligand · 2 copies · chains A, C, G, P
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, G, Q
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, G, Q
- CA · Calcium ion · metal · 2 copies · chains O, f
- CL · Chloride ion · ion · 2 copies · chains A, D, G, Q
- LMT · Dodecyl-beta-D-maltoside · additive · 14 copies · chains B, D, H, G, g, a, f, X, I, M, e, A, T, N, O, Q, W, 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 | 1013 | 0.87 | 0.87 | 80 | CLA, BCR |
| 2 | 1005 | 0.87 | 0.87 | 81 | BCR, CLA |
| 3 | 1069 | 0.85 | 0.86 | 89 | HEM |
| 4 | 1126 | 0.84 | 0.85 | 99 | HEM |
| 5 | 798 | 0.84 | 0.86 | 80 | LMG, PL9 |
Interfaces
135 interfaces between chains.
- A–D · 5552 Ų buried · 64 hydrogen bonds · protein-protein
- G–Q · 5545 Ų buried · 65 hydrogen bonds · protein-protein
- A–C · 3298 Ų buried · 41 hydrogen bonds · protein-protein
- G–P · 3295 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 2654 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4FBY · fs X-ray diffraction of Photosystem II · the same entry in another collection · chain L against L, 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 P0A444
- Every structure of UniProt Q8DIQ1
- Every structure of UniProt Q8DIF8
- Every structure of UniProt Q8CM25
- Every structure of UniProt Q8DIP0
- Every structure of UniProt Q8DIN9
- Every structure of UniProt Q8DJ43
- Every structure of UniProt Q8DJZ6
- Every structure of UniProt P59087
- Every structure of UniProt Q9F1K9
- Every structure of UniProt Q8DIN8
- Every structure of UniProt Q8DHA7
- Every structure of UniProt P0A431
- Every structure of UniProt Q8DIQ0
- Every structure of UniProt Q9F1L5
- Every structure of UniProt P0A386
- Every structure of UniProt Q8DJI1
- Every structure of UniProt Q9F1R6
- Every structure of UniProt Q8DHJ2
- Elsewhere: RCSB PDB 4FBY · PDBe 4FBY · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt Q8DIP0 · UniProt Q8DIN9 · UniProt Q8DJ43 · UniProt Q8DJZ6 · UniProt P59087 · UniProt Q9F1K9 · UniProt Q8DIN8 · UniProt Q8DHA7 · UniProt P0A431 · UniProt Q8DIQ0 · UniProt Q9F1L5 · UniProt P0A386 · UniProt Q8DJI1 · UniProt Q9F1R6 · UniProt Q8DHJ2
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