MolNFT v1 · #175792 · protein
Cryo-EM structure of psii at 2.08 ångström resolution
7D1U · Photosystem II protein D1: “Cryo-EM structure of psii at 2.08 ångström resolution”. Electron microscopy, 17 ligands (CLA, UNL, BCR), 20 pockets (best druggability 0.87). MolNFT v1 #175792 on GenesisL1: 3D structure, binding sites…
- PDB
- 7D1U
- Type
- protein
- Length
- 5,312 residues
- Chains
- 40
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II protein D1; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P51765, D0VWR1, D0VWR7, D0VWR8, P12238, P12239, P19052, P12240, Q7DGD4, P19054, P12241, P12312, D0VWR2, P12313, P56152, P0A387, D0VWR3, D0VWR4, D0VWR5, P0DM37
- Ligands
- CLA, UNL, BCR, LMG, LHG, SQD, DGD, PHO, PL9, OEX, BCT, HEM, RRX, HEC, FE2, MG…
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 20 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 (EC 1.10.3.9) | protein | 334 | 60% helix, 4% strand | P51765 |
| B, b | Photosystem II CP47 reaction center protein | protein | 504 | 50% helix, 10% strand | D0VWR1 |
| C, c | Photosystem II CP43 reaction center protein | protein | 451 | 57% helix, 6% strand | D0VWR7 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 341 | 62% helix, 4% strand | D0VWR8 |
| E, e | Cytochrome B559 subunit alpha | protein | 81 | 54% helix, 0% strand | P12238 |
| F, f | Cytochrome B559 subunit beta | protein | 34 | 68% helix, 0% strand | P12239 |
| H, h | Photosystem II reaction center protein H | protein | 63 | 51% helix, 3% strand | P19052 |
| I, i | Photosystem II reaction center protein I | protein | 36 | 69% helix, 0% strand | P12240 |
| J, j | Photosystem II reaction center protein J | protein | 36 | 61% helix, 0% strand | Q7DGD4 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 76% helix, 0% strand | P19054 |
| L, l | Photosystem II reaction center protein L | protein | 37 | 62% helix, 3% strand | P12241 |
| M, m | Photosystem II reaction center protein M | protein | 33 | 73% helix, 0% strand | P12312 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 244 | 5% helix, 45% strand | D0VWR2 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | P12313 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 97 | 48% helix, 4% strand | P56152 |
| V, v | Cytochrome C-550 | protein | 137 | 48% helix, 6% strand | P0A387 |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 27 | 78% helix, 0% strand | D0VWR3 |
| X, x | Photosystem II reaction center protein X | protein | 38 | 79% helix, 0% strand | D0VWR4 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 81% helix, 0% strand | D0VWR5 |
| R, r | Photosystem II protein Y | protein | 34 | 91% helix, 0% strand | P0DM37 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, F, I, B, H, L, M, t, C, K, Y, Z, X, a, d, f, i, b, h, l, m, c, k, y, z, x
- UNL · Unknown ligand · ligand · 36 copies · chains A, I, B, D, H, X, a, o, C, E, F, J, Y, K, M, T, b, m, i, O, d, h, x, c, e, f, j, y, k, t
- BCR · Beta-carotene · ligand · 20 copies · chains A, I, B, M, t, a, C, K, Z, D, F, J, T, b, Y, i, m, c, k, z, d, f, j, y
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 10 copies · chains B, D, L, M, A, C, I, J, K, Y, Z, F, b, d, l, m, a, c, i, 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, b, d, l, m, t, c, e, f
- 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, h, E, F, X, R, L, M, l, a, c, d, j, k, B, H, t, e, f, x, r, m
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 8 copies · chains A, C, J, D, V, B, H, a, c, j, d, v, b, h
- 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
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, R, e, f, r
- RRX · (3R)-beta,beta-caroten-3-ol · ligand · 2 copies · chains H, X, h, x
- HEC · Heme C · ligand · 2 copies · chains C, V, c, 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 · 4 copies · chains A, D, C, a, d, c
- LMT · Dodecyl-beta-D-maltoside · additive · 8 copies · chains A, C, I, J, M, l, m, Z, a, c, i, j, L, z
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 | 1153 | 0.87 | 0.87 | 84 | CLA, BCR |
| 2 | 1200 | 0.87 | 0.87 | 90 | CLA, BCR |
| 3 | 923 | 0.85 | 0.87 | 85 | HEC |
| 4 | 947 | 0.85 | 0.86 | 93 | HEC |
| 5 | 928 | 0.85 | 0.85 | 103 | LHG, PL9 |
Interfaces
135 interfaces between chains.
- a–d · 5436 Ų buried · 75 hydrogen bonds · protein-protein
- A–D · 5429 Ų buried · 75 hydrogen bonds · protein-protein
- A–C · 3280 Ų buried · 40 hydrogen bonds · protein-protein
- a–c · 3274 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 3020 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 cofactor, 2 disulfide (formylation, heme c attachment, disulfide, nonstandard).
Compared structures
- 7D1U · Cryo-EM Structure of PSII at 2.08 angstrom resolution · 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 P51765
- Every structure of UniProt D0VWR1
- Every structure of UniProt D0VWR7
- Every structure of UniProt D0VWR8
- Every structure of UniProt P12238
- Every structure of UniProt P12239
- Every structure of UniProt P19052
- Every structure of UniProt P12240
- Every structure of UniProt Q7DGD4
- Every structure of UniProt P19054
- Every structure of UniProt P12241
- Every structure of UniProt P12312
- Every structure of UniProt D0VWR2
- Every structure of UniProt P12313
- Every structure of UniProt P56152
- Every structure of UniProt P0A387
- Every structure of UniProt D0VWR3
- Every structure of UniProt D0VWR4
- Every structure of UniProt D0VWR5
- Every structure of UniProt P0DM37
- Elsewhere: RCSB PDB 7D1U · PDBe 7D1U · UniProt P51765 · UniProt D0VWR1 · UniProt D0VWR7 · UniProt D0VWR8 · UniProt P12238 · UniProt P12239 · UniProt P19052 · UniProt P12240 · UniProt Q7DGD4 · UniProt P19054 · UniProt P12241 · UniProt P12312 · UniProt D0VWR2 · UniProt P12313 · UniProt P56152 · UniProt P0A387 · UniProt D0VWR3 · UniProt D0VWR4 · UniProt D0VWR5 · UniProt P0DM37
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