MolNFT v1 · #117410 · protein
Macromolecular diffractive imaging using imperfect crystals - bragg data
5E7C · Photosystem II protein D1 1: “Macromolecular diffractive imaging using imperfect crystals - bragg data”. X-ray diffraction, 15 ligands (CLA, BCR, LMG), 20 pockets (best druggability 0.88). MolNFT v1 #117410 on GenesisL1: 3D…
- PDB
- 5E7C
- Type
- protein
- Length
- 5,264 residues
- Chains
- 38
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II protein D1 1; Photosystem II CP47 reaction center 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, LHG, DGD, SQD, PHO, PL9, HEM, OEX, BCT, CA, FE2, MG, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 19 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 1 (EC 1.10.3.9) | protein | 334 | 60% helix, 4% strand | P0A444 |
| B, b | Photosystem II CP47 reaction center protein | protein | 504 | 50% helix, 11% strand | Q8DIQ1 |
| C, c | Photosystem II CP43 reaction center protein | protein | 451 | 58% helix, 6% strand | Q8DIF8 |
| D, 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 | 54% helix, 1% strand | Q8DIP0 |
| F, f | Cytochrome B559 subunit beta | protein | 34 | 68% helix, 0% strand | Q8DIN9 |
| H, h | Photosystem II reaction center protein H | protein | 65 | 54% helix, 6% strand | Q8DJ43 |
| I, i | Photosystem II reaction center protein I | protein | 38 | 68% helix, 0% strand | Q8DJZ6 |
| J, j | Photosystem II reaction center protein J | protein | 38 | 61% helix, 3% 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, 5% 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, 47% 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 | 52% helix, 4% 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 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, F, I, B, H, L, M, m, t, C, K, Y, Z, X, a, d, f, i, l, b, h, c, k, y, z, x
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, K, Z, D, F, J, H, X, Y, T, b, a, i, m, c, k, z, d, f, j, h, x, y
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains A, C, I, B, D, L, M, J, K, Y, Z, F, a, c, i, b, d, l, m, j, k, y, z, f
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 10 copies · chains A, B, D, L, M, T, C, E, F, a, c, d, b, l, m, t, e, f
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains A, C, J, D, V, E, B, H, a, c, j, d, v, e, b, h
- 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, B, L, l, m, t, E, F, X, a, c, d, j, k, T, b, M, e, f, x
- 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 · 6 copies · chains B, O, F, V, b, o, f, v
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- MG · Magnesium ion · metal · 2 copies · chains F, J, 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 | 1014 | 0.88 | 0.88 | 79 | CLA, BCR |
| 2 | 1159 | 0.87 | 0.87 | 86 | CLA, BCR |
| 3 | 811 | 0.85 | 0.88 | 87 | HEM |
| 4 | 925 | 0.85 | 0.86 | 94 | HEM |
| 5 | 800 | 0.83 | 0.86 | 99 | PL9, LHG |
Interfaces
133 interfaces between chains.
- a–d · 5491 Ų buried · 69 hydrogen bonds · protein-protein
- A–D · 5467 Ų buried · 68 hydrogen bonds · protein-protein
- A–C · 3314 Ų buried · 42 hydrogen bonds · protein-protein
- a–c · 3298 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 3100 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- Q8DIQ1 · AlphaFold monomer V2.0 prediction for photosystem II CP47 reaction center protein (Q8DIQ1) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q8CM25 · AlphaFold monomer V2.0 prediction for photosystem II D2 protein (Q8CM25) · a predicted model of the same protein · chain D against A, TM-score 1.00
- Q8DIF8 · AlphaFold monomer V2.0 prediction for photosystem II CP43 reaction center protein (Q8DIF8) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P0A444 · AlphaFold monomer V2.0 prediction for photosystem II protein D1 1 (P0A444) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P0A386 · AlphaFold monomer V2.0 prediction for cytochrome C-550 (P0A386) · a predicted model of the same protein · chain V against A, TM-score 1.00
- P0A431 · AlphaFold monomer V2.0 prediction for photosystem II manganese- stabilizing polypeptide… · a predicted model of the same protein · chain O against A, TM-score 1.00
- Q9F1L5 · AlphaFold monomer V2.0 prediction for photosystem II 12 kda extrinsic protein (Q9F1L5) · a predicted model of the same protein · chain U against A, TM-score 0.99
- P59087 · AlphaFold monomer V2.0 prediction for photosystem II reaction center protein J (P59087) · a predicted model of the same protein · chain J against A, TM-score 0.96
- Q8DIP0 · AlphaFold monomer V2.0 prediction for cytochrome B559 subunit alpha (Q8DIP0) · a predicted model of the same protein · chain E against A, TM-score 0.94
- Q8DJ43 · AlphaFold monomer V2.0 prediction for photosystem II reaction center protein H (Q8DJ43) · a predicted model of the same protein · chain H against A, TM-score 0.93
- Q8DHJ2 · AlphaFold monomer V2.0 prediction for photosystem II reaction center protein Z (Q8DHJ2) · a predicted model of the same protein · chain Z against A, TM-score 0.92
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 5E7C · PDBe 5E7C · 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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