MolNFT v1 · #103276 · protein
Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser the S1 state
4PBU · Photosystem Q(B) protein 1: “Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser the S1 state”. X-ray diffraction, 14 ligands (CLA, BCR, LHG), 20 pockets (best druggability 0.87). MolNFT v1 #103276…
- PDB
- 4PBU
- Type
- protein
- Length
- 5,267 residues
- Chains
- 38
- 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, LHG, DGD, SQD, PHO, PL9, HEM, OEX, BCT, CA, FE2, MG, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 23 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem Q(B) protein 1 (EC 1.10.3.9) | protein | 334 | 60% helix, 4% strand | P0A444 |
| B, b | Photosystem II core light harvesting protein | protein | 504 | 50% helix, 11% strand | Q8DIQ1 |
| C | Photosystem II CP43 protein | protein | 451 | 58% helix, 6% strand | Q8DIF8 |
| D | Photosystem II D2 protein (EC 1.10.3.9) | protein | 342 | 63% helix, 4% strand | Q8CM25 |
| E, e | Cytochrome B559 subunit alpha | protein | 81 | 53% helix, 0% strand | Q8DIP0 |
| F | Cytochrome B559 subunit beta | protein | 34 | 68% helix, 0% strand | Q8DIN9 |
| H, h | Photosystem II reaction center protein H | protein | 65 | 49% helix, 3% strand | Q8DJ43 |
| I, i | Photosystem II reaction center protein I | protein | 38 | 68% helix, 0% strand | Q8DJZ6 |
| J | Photosystem II reaction center protein J | protein | 38 | 61% helix, 0% strand | P59087 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 81% helix, 0% strand | Q9F1K9 |
| L, l | Photosystem II reaction center protein L | protein | 37 | 62% helix, 3% strand | Q8DIN8 |
| M, m | Photosystem II reaction center protein M | protein | 34 | 71% helix, 0% strand | Q8DHA7 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 243 | 6% helix, 46% strand | P0A431 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | Q8DIQ0 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 97 | 49% helix, 5% strand | Q9F1L5 |
| V, v | Cytochrome C-550 | protein | 137 | 46% helix, 6% strand | P0A386 |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 29 | 79% helix, 0% strand | Q8DJI1 |
| X, x | Photosystem II reaction center X protein | protein | 39 | 77% helix, 0% strand | Q9F1R6 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 89% helix, 0% strand | Q8DHJ2 |
| c | Photosystem II CP43 protein | protein | 455 | 58% helix, 6% strand | Q8DIF8 |
| d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 341 | 65% helix, 4% strand | Q8CM25 |
| f | Cytochrome B559 subunit beta | protein | 32 | 72% helix, 0% strand | Q8DIN9 |
| j | Photosystem II reaction center protein J | protein | 40 | 55% helix, 0% strand | P59087 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, F, I, L, B, H, M, m, t, C, K, Y, Z, X, a, d, f, i, b, h, l, c, k, y, z, x
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, b, B, M, t, a, C, K, Z, D, F, J, H, X, T, m, Y, i, c, k, z, d, f, j, h, x, y
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 10 copies · chains A, D, E, F, B, L, M, T, C, a, d, e, f, b, l, m, t, c
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains A, C, J, D, V, E, F, B, H, a, c, j, d, e, f, b, h, v
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 8 copies · chains A, C, D, J, K, T, b, E, F, X, L, M, l, B, a, t, c, d, j, k, e, f, x, m
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- 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 · 4 copies · chains A, D, F, X, L, T, a, d, f, x, l, t
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F, C, V, e, f, c, v
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- CA · Calcium ion · metal · 7 copies · chains B, F, V, O, b, c, f, v, o
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- MG · Magnesium ion · metal · chains f, j
- CL · Chloride ion · ion · 6 copies · chains A, D, C, U, V, a, d, c, u, v
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 | 1048 | 0.87 | 0.88 | 80 | CLA, BCR |
| 2 | 965 | 0.87 | 0.88 | 78 | CLA, BCR |
| 3 | 881 | 0.86 | 0.87 | 87 | HEM |
| 4 | 952 | 0.85 | 0.86 | 100 | HEM |
| 5 | 870 | 0.84 | 0.86 | 99 | LHG, PL9 |
Interfaces
133 interfaces between chains.
- a–d · 5529 Ų buried · 69 hydrogen bonds · protein-protein
- A–D · 5492 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 3306 Ų buried · 44 hydrogen bonds · protein-protein
- a–c · 3296 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 3099 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide (heme attachment, disulfide).
Compared structures
- 4PBU · Serial Time-resolved crystallography of Photosystem II using a femtosecond X-ray laser… · the same entry in another collection · chain E against E, 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 4PBU · PDBe 4PBU · 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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