Research workbench
Structure of sr-substituted photosystem II
Analyse Structure of sr-substituted photosystem II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IL6
- Type
- protein
- Length
- 5,288 residues
- Chains
- 39
- 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…
- EC
- 1.10.3.9
- UniProt
- P51765, P12238, P12239, Q7DGD4, P12241, P12313, P0A387, Q8DKM3
- Ligands
- CLA, UNL, BCR, LMG, LHG, SQD, DGD, PHO, PL9, HEM, OER, BCT, MG, FE2, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 26 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Photosystem Q(B) protein (EC 1.10.3.9) | protein | 334 | 60% helix, 4% strand | P51765 |
| B, b | Photosystem II core light harvesting protein | protein | 505 | 50% helix, 11% strand | — |
| C | Photosystem II CP43 protein | protein | 451 | 57% helix, 6% strand | — |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 342 | 62% helix, 4% strand | — |
| E | Cytochrome B559 subunit alpha | protein | 80 | 55% helix, 0% strand | P12238 |
| 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 | — |
| I, i | Photosystem II reaction center protein I | protein | 36 | 64% helix, 0% strand | — |
| J, j | Photosystem II reaction center protein J | protein | 37 | 59% 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 | 37 | 62% helix, 5% strand | P12241 |
| M, m | Photosystem II reaction center protein M | protein | 34 | 71% helix, 0% strand | — |
| O | Photosystem II manganese-stabilizing polypeptide | protein | 244 | 6% helix, 46% strand | — |
| T | Photosystem II reaction center protein T | protein | 31 | 68% helix, 0% strand | P12313 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 97 | 49% helix, 4% strand | — |
| V, v | Cytochrome C-550 | protein | 137 | 47% helix, 6% strand | P0A387 |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 30 | 80% helix, 0% strand | — |
| X | Photosystem II reaction center protein X | protein | 40 | 75% helix, 0% strand | — |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 87% helix, 0% strand | — |
| R | Photosystem II protein Y | protein | 34 | 88% helix, 0% strand | Q8DKM3 |
| c | Photosystem II CP43 protein | protein | 450 | 58% helix, 6% strand | — |
| e | Cytochrome B559 subunit alpha | protein | 78 | 55% helix, 0% strand | P12238 |
| f | Cytochrome B559 subunit beta | protein | 32 | 72% helix, 0% strand | P12239 |
| o | Photosystem II manganese-stabilizing polypeptide | protein | 243 | 6% helix, 46% strand | — |
| t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | P12313 |
| x | Photosystem II reaction center protein X | protein | 39 | 77% helix, 0% strand | — |
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, l, i, b, h, m, c, k, y, z, x
- UNL · Unknown ligand · ligand · 24 copies · chains A, B, D, H, X, I, J, C, K, L, m, Y, a, b, c, d, k, h, x, i, j, M, l, t, y
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, D, F, J, H, X, K, Y, Z, T, b, a, i, m, c, d, f, j, h, x, k, z, 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, j, k, y, z, d, f, b, l, m
- 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, B, L, l, m, t, E, F, X, R, a, M, 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
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F, R, C, V, e, f, c, v
- OER · Sr-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- MG · Magnesium ion · metal · 4 copies · chains F, J, K, Y, f, j, k, y
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 4 copies · chains A, D, C, a, d, c
- DMS · Dimethyl sulfoxide · additive · 35 copies · chains A, D, O, b, B, U, H, C, V, a, d, o, u, h, c, v
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 17 copies · chains B, a, C, D, H, X, E, R, V, A, b, O, c, d, h, x, e, o
- LMT · Dodecyl-beta-D-maltoside · additive · 15 copies · chains A, D, M, b, I, B, H, X, C, m, t, l, a, d, c, i, h, x, T, e, f, j, L
- GOL · Glycerol · additive · 12 copies · chains A, O, B, D, V, F, a, b, d, v, f
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 | 1023 | 0.87 | 0.88 | 75 | CLA, BCR |
| 2 | 860 | 0.86 | 0.88 | 75 | DMS, HEM |
| 3 | 1179 | 0.86 | 0.86 | 83 | CLA, BCR |
| 4 | 1022 | 0.84 | 0.85 | 99 | DMS, HEM |
| 5 | 762 | 0.84 | 0.86 | 85 | LHG |
Interfaces
134 interfaces between chains.
- a–d · 5490 Ų buried · 70 hydrogen bonds · protein-protein
- A–D · 5478 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 3297 Ų buried · 39 hydrogen bonds · protein-protein
- a–c · 3290 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 3024 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 cofactor, 2 disulfide (formylation, heme attachment, disulfide).
Compared structures
- 4IL6 · Structure of Sr-substituted photosystem II · 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
- Every structure of UniProt Q8DKM3
- Elsewhere: RCSB PDB 4IL6 · PDBe 4IL6 · UniProt P51765 · UniProt P12238 · UniProt P12239 · UniProt Q7DGD4 · UniProt P12241 · UniProt P12313 · UniProt P0A387 · UniProt Q8DKM3
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