MolNFT v1 · #57206 · protein
Crystal structure of I-substituted photosystem II complex
3A0H · Photosystem Q(B) protein: “Crystal structure of I-substituted photosystem II complex”. X-ray diffraction, 11 ligands (CLA, BCR, DGD), 20 pockets (best druggability 0.85). MolNFT v1 #57206 on GenesisL1: 3D structure, binding sites…
- PDB
- 3A0H
- Type
- protein
- Length
- 5,246 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem Q(B) protein; Photosystem II core light harvesting protein; Photosystem II…
- UniProt
- P51765, P12238, P12239, Q7DGD4, P12241, P12313, P0A387
- Ligands
- CLA, BCR, DGD, MGE, PHO, PQ9, HEM, OEC, LHG, FE2, IOD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 20 distinct chains · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem Q(B) protein | protein | 335 | 55% helix, 2% strand | P51765 |
| B, b | Photosystem II core light harvesting protein | protein | 488 | 42% helix, 10% strand | — |
| C, c | Photosystem II CP43 protein | protein | 447 | 48% helix, 4% strand | — |
| D, d | Photosystem II D2 protein | protein | 340 | 56% helix, 2% strand | — |
| E, e | Cytochrome B559 subunit alpha | protein | 82 | 57% helix, 0% strand | P12238 |
| F, f | Cytochrome B559 subunit beta | protein | 35 | 66% helix, 0% strand | P12239 |
| H, h | Photosystem II reaction center protein H | protein | 64 | 52% helix, 0% strand | — |
| I, i | Photosystem II reaction center protein I | protein | 35 | 66% helix, 0% strand | — |
| J, j | Photosystem II reaction center protein J | protein | 34 | 62% helix, 0% strand | Q7DGD4 |
| K, k | Photosystem II reaction center protein K | protein | 36 | 83% helix, 0% strand | — |
| L, l | Photosystem II reaction center protein L | protein | 37 | 54% helix, 3% strand | P12241 |
| M, m | Photosystem II reaction center protein M | protein | 36 | 58% helix, 0% strand | — |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 242 | 3% helix, 40% strand | — |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | P12313 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 98 | 42% helix, 4% strand | — |
| V, v | Cytochrome C-550 | protein | 137 | 39% helix, 3% strand | P0A387 |
| X, x | Photosystem II reaction center protein X | protein | 34 | 85% helix, 0% strand | — |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 28 | 75% helix, 0% strand | — |
| N, n | Photosystem II reaction center protein Y | protein | 23 | 78% helix, 0% strand | — |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 84% helix, 0% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, L, I, B, H, M, m, C, K, J, Y, Z, X, a, d, t, l, i, b, h, c, k, j, y, z, x
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, K, Z, D, F, J, H, X, T, b, Y, a, i, m, c, k, z, d, f, j, h, x, y
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 8 copies · chains A, C, J, D, V, B, H, a, c, j, d, v, b, h
- MGE · (1S)-2-(alpha-L-allopyranosyloxy)-1-[(tridecanoyloxy) methyl]ethyl palmitate · ligand · 8 copies · chains D, F, J, A, B, L, T, M, d, f, j, a, b, l, t, m
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- PQ9 · 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18,22,26-heptaenyl]-2,3-dimethylbenzo-1,4-quinone · ligand · 4 copies · chains A, D, F, L, a, d, f, l
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F, N, C, V, e, f, n, c, v
- OEC · Oxygen evolving system · ligand · 2 copies · chains A, C, a, c
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains A, C, D, a, c, d
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- IOD · Iodide ion · ion · 10 copies · chains A, D, C, B, T, a, d, c, b, t
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 | 964 | 0.85 | 0.86 | 89 | HEM |
| 2 | 900 | 0.85 | 0.86 | 53 | BCR |
| 3 | 1176 | 0.85 | 0.85 | 81 | CLA, BCR |
| 4 | 1036 | 0.84 | 0.85 | 91 | HEM |
| 5 | 748 | 0.82 | 0.85 | 91 | PQ9, MGE |
Interfaces
137 interfaces between chains.
- A–D · 5458 Ų buried · 66 hydrogen bonds · protein-protein
- a–d · 5440 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 3141 Ų buried · 32 hydrogen bonds · protein-protein
- a–c · 3136 Ų buried · 32 hydrogen bonds · protein-protein
- b–d · 2642 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3A0H · Crystal structure of I-substituted Photosystem II complex · 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 P12238
- Every structure of UniProt P12239
- Every structure of UniProt Q7DGD4
- Every structure of UniProt P12241
- Every structure of UniProt P12313
- Every structure of UniProt P0A387
- Elsewhere: RCSB PDB 3A0H · PDBe 3A0H · UniProt P51765 · UniProt P12238 · UniProt P12239 · UniProt Q7DGD4 · UniProt P12241 · UniProt P12313 · UniProt P0A387
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