MolNFT v1 · #120228 · protein
Native xfel structure of photosystem II (dark dataset)
5GTH · Photosystem II protein D1: “Native xfel structure of photosystem II (dark dataset)”. X-ray diffraction, 17 ligands (CLA, BCR, UNL), 20 pockets (best druggability 0.87). MolNFT v1 #120228 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GTH
- Type
- protein
- Length
- 5,290 residues
- Chains
- 39
- Method
- x-ray diffraction
- 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
- D0VWR1, D0VWR8, P12238, P12239, P19052, P12240, Q7DGD4, P12241, D0VWR2, P12313, P56152, P0A387, D0VWR4, D0VWR3, D0VWR5, P0DM37
- Ligands
- CLA, BCR, UNL, LMG, LHG, SQD, DGD, PHO, PL9, OEX, BCT, HEM, HEC, CA, FE2, MG, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 28 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem II protein D1 (EC 1.10.3.9) | protein | 334 | 59% helix, 4% strand | — |
| B, b | Photosystem II CP47 reaction center protein | protein | 504 | 51% helix, 10% strand | D0VWR1 |
| C | Photosystem II CP43 reaction center protein | protein | 451 | 58% helix, 6% strand | — |
| D | Photosystem II D2 protein (EC 1.10.3.9) | protein | 342 | 64% helix, 3% strand | D0VWR8 |
| E | Cytochrome B559 subunit alpha | protein | 81 | 54% helix, 0% strand | P12238 |
| F | Cytochrome B559 subunit beta | protein | 34 | 68% helix, 0% strand | P12239 |
| H | Photosystem II reaction center protein H | protein | 64 | 56% helix, 3% strand | P19052 |
| I, i | Photosystem II reaction center protein I | protein | 38 | 68% helix, 0% strand | P12240 |
| J | Photosystem II reaction center protein J | protein | 38 | 58% helix, 0% strand | Q7DGD4 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 76% helix, 0% strand | — |
| L, l | Photosystem II reaction center protein L | protein | 36 | 64% helix, 3% strand | P12241 |
| M | Photosystem II reaction center protein M | protein | 33 | 76% helix, 0% strand | — |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 243 | 6% helix, 47% strand | D0VWR2 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | P12313 |
| U | Photosystem II 12 kda extrinsic protein | protein | 96 | 50% helix, 4% strand | P56152 |
| V, v | Cytochrome C-550 | protein | 137 | 45% helix, 6% strand | P0A387 |
| X, x | Photosystem II reaction center protein X | protein | 38 | 79% helix, 0% strand | D0VWR4 |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 29 | 79% helix, 0% strand | D0VWR3 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 87% helix, 0% strand | D0VWR5 |
| R | Photosystem II protein Y | protein | 34 | 94% helix, 0% strand | P0DM37 |
| c | Photosystem II CP43 reaction center protein | protein | 455 | 56% helix, 6% strand | — |
| d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 341 | 64% helix, 4% strand | D0VWR8 |
| e | Cytochrome B559 subunit alpha | protein | 79 | 54% helix, 0% strand | P12238 |
| f | Cytochrome B559 subunit beta | protein | 31 | 74% helix, 0% strand | P12239 |
| h | Photosystem II reaction center protein H | protein | 65 | 55% helix, 3% strand | P19052 |
| j | Photosystem II reaction center protein J | protein | 39 | 56% helix, 0% strand | Q7DGD4 |
| m | Photosystem II reaction center protein M | protein | 34 | 74% helix, 0% strand | — |
| u | Photosystem II 12 kda extrinsic protein | protein | 97 | 51% helix, 4% strand | P56152 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, L, F, I, B, H, M, t, C, K, Y, Z, X, a, d, i, b, h, l, m, 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, T, b, Y, a, i, m, c, k, z, d, f, j, h, x, y
- UNL · Unknown ligand · ligand · 18 copies · chains A, B, D, H, X, I, J, C, K, M, a, b, d, h, x, c, k, i, j, m
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains B, D, L, M, A, C, I, J, K, Y, F, Z, 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, 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, B, L, l, m, t, E, F, X, R, M, a, c, d, j, k, e, f, x
- 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
- HEC · Heme C · ligand · 2 copies · chains C, V, c, v
- CA · Calcium ion · metal · 6 copies · chains C, O, A, F, V, c, o
- 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
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 15 copies · chains B, a, o, O, C, D, H, V, b, A, c, d, h
- LMT · Dodecyl-beta-D-maltoside · additive · 14 copies · chains B, a, m, t, d, o, M, A, D, O, b, H, X, E, F, J, C, I, l, T, c, i, h, e, f, j, L
- GOL · Glycerol · additive · 7 copies · chains A, b, B, D, C, V, a, h, d, l, m, 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 | 999 | 0.87 | 0.88 | 74 | CLA, BCR |
| 2 | 994 | 0.87 | 0.87 | 82 | CLA, BCR |
| 3 | 995 | 0.85 | 0.86 | 86 | HEC |
| 4 | 1005 | 0.85 | 0.86 | 89 | HEC |
| 5 | 727 | 0.83 | 0.86 | 83 | LHG |
Interfaces
130 interfaces between chains.
- A–D · 5436 Ų buried · 65 hydrogen bonds · protein-protein
- a–d · 5425 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 3272 Ų buried · 38 hydrogen bonds · protein-protein
- a–c · 3262 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 3017 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 cofactor, 2 disulfide (formylation, heme c attachment, disulfide).
Compared structures
- 5GTH · Native XFEL structure of photosystem II (dark dataset) · the same entry in another collection · chain d against d, 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 D0VWR1
- 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 P12241
- Every structure of UniProt D0VWR2
- Every structure of UniProt P12313
- Every structure of UniProt P56152
- Every structure of UniProt P0A387
- Every structure of UniProt D0VWR4
- Every structure of UniProt D0VWR3
- Every structure of UniProt D0VWR5
- Every structure of UniProt P0DM37
- Elsewhere: RCSB PDB 5GTH · PDBe 5GTH · UniProt D0VWR1 · UniProt D0VWR8 · UniProt P12238 · UniProt P12239 · UniProt P19052 · UniProt P12240 · UniProt Q7DGD4 · UniProt P12241 · UniProt D0VWR2 · UniProt P12313 · UniProt P56152 · UniProt P0A387 · UniProt D0VWR4 · UniProt D0VWR3 · UniProt D0VWR5 · UniProt P0DM37
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