Research workbench
Re-refinement of crystal structure of photosystem II complex
Analyse Re-refinement of crystal structure of photosystem II complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V2C
- Type
- protein
- Length
- 5,280 residues
- Chains
- 38
- 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
- P51765, D0VWR1, D0VWR7, D0VWR8, P12238, P12239, P19052, P12240, Q7DGD4, P19054, P12241, P12312, D0VWR2, P12313, P56152, P0A387, D0VWR3, D0VWR4, D0VWR5
- Ligands
- CLA, BCR, LMG, LHG, SQD, DGD, PHO, PL9, BCT, OEX, HEM, HEC, CA, MG, FE2, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 23 distinct chains · 54% 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 | Photosystem II CP47 reaction center protein | protein | 504 | 50% helix, 11% strand | D0VWR1 |
| C | Photosystem II CP43 reaction center protein | protein | 451 | 58% helix, 6% strand | D0VWR7 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 342 | 65% helix, 4% strand | D0VWR8 |
| E, e | Cytochrome B559 subunit alpha | protein | 81 | 57% 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 | 65 | 51% helix, 3% strand | P19052 |
| I, i | Photosystem II reaction center protein I | protein | 38 | 61% helix, 0% strand | P12240 |
| J, j | Photosystem II reaction center protein J | protein | 39 | 56% helix, 0% strand | Q7DGD4 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 81% helix, 0% strand | P19054 |
| L, l | Photosystem II reaction center protein L | protein | 37 | 62% helix, 5% strand | P12241 |
| M | Photosystem II reaction center protein M | protein | 34 | 71% helix, 0% strand | P12312 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 245 | 6% helix, 46% 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 | 51% helix, 4% strand | P56152 |
| V, v | Cytochrome C-550 | protein | 137 | 46% helix, 6% strand | P0A387 |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 29 | 79% helix, 0% strand | D0VWR3 |
| X, x | Photosystem II reaction center protein X | protein | 40 | 75% helix, 0% strand | D0VWR4 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 89% helix, 0% strand | D0VWR5 |
| b | Photosystem II CP47 reaction center protein | protein | 506 | 50% helix, 11% strand | D0VWR1 |
| c | Photosystem II CP43 reaction center protein | protein | 458 | 57% helix, 6% strand | D0VWR7 |
| f | Cytochrome B559 subunit beta | protein | 32 | 72% helix, 0% strand | P12239 |
| m | Photosystem II reaction center protein M | protein | 35 | 69% helix, 0% strand | P12312 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, I, B, H, L, M, C, K, Y, Z, X, a, d, t, i, b, h, l, m, c, k, y, z, x
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, b, B, M, t, C, K, Z, D, F, J, H, X, Y, T, a, i, m, c, k, z, d, f, j, h, x, y
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 14 copies · chains A, C, I, B, D, L, M, H, X, J, K, Y, Z, F, a, c, i, b, d, l, m, j, k, y, z, h, x, f
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 12 copies · chains A, C, K, B, D, L, M, T, E, F, a, c, k, b, d, l, m, t, e, f
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 11 copies · chains A, C, D, J, K, T, b, I, E, F, X, a, c, d, j, k, B, t, i, L, M, l, h, m, e, f, x
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains A, C, J, D, V, E, F, B, H, a, c, j, d, v, e, f, 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
- BCT · Bicarbonate ion · ligand · 3 copies · chains A, D, a, d, M, m
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, e, f
- HEC · Heme C · ligand · 2 copies · chains C, V, c, v
- CA · Calcium ion · metal · 6 copies · chains B, O, b, c, h, o
- MG · Magnesium ion · metal · 4 copies · chains F, V, J, f, v, j
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 6 copies · chains A, D, C, U, V, a, d, c, u, v
- PGE · Triethylene glycol · additive · 65 copies · chains A, b, J, B, D, V, C, X, E, H, I, O, T, U, Y, Z, a, i, c, L, t, d, h, x, j, o, u, M
- GOL · Glycerol · additive · 60 copies · chains A, O, b, D, E, V, B, U, H, M, t, C, L, T, X, F, a, o, d, e, v, u, h, m, c, y, l, f, j
- PG4 · Tetraethylene glycol · additive · 57 copies · chains A, B, H, C, D, X, E, J, I, Y, K, U, V, a, t, b, h, c, j, k, d, x, e, i, M, l
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 24 copies · chains B, O, a, C, D, H, A, b, V, c, t, o, d, h
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, L, H, C, D, E, J, I, O, V, X, a, c, b, d, o, e, i
- LMT · Dodecyl-beta-D-maltoside · additive · 18 copies · chains A, D, O, b, B, H, X, C, I, E, F, J, M, l, m, T, Y, a, d, o, h, x, c, i, e, f, j, y, t, L, u
- P6G · Hexaethylene glycol · additive · 17 copies · chains A, I, T, B, C, D, H, X, F, E, b, c, d, h, x, j
- 1PE · Pentaethylene glycol · additive · 7 copies · chains B, L, m, V, e, f, j, x
- 2PE · Nonaethylene glycol · additive · chains V
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains a, i
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 | 1037 | 0.87 | 0.88 | 78 | CLA, BCR |
| 2 | 993 | 0.87 | 0.87 | 77 | CLA, BCR |
| 3 | 929 | 0.85 | 0.86 | 96 | GOL, HEC |
| 4 | 1007 | 0.85 | 0.85 | 95 | GOL, HEC |
| 5 | 1024 | 0.83 | 0.84 | 139 | DGD, GOL, BCR, LMG, MG |
Interfaces
132 interfaces between chains.
- A–D · 5478 Ų buried · 69 hydrogen bonds · protein-protein
- a–d · 5462 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 3261 Ų buried · 37 hydrogen bonds · protein-protein
- a–c · 3258 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 3040 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 cofactor, 2 disulfide (formylation, heme c attachment, disulfide, methylation).
Compared structures
- 5V2C · Re-refinement of crystal structure of 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 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
- Elsewhere: RCSB PDB 5V2C · PDBe 5V2C · 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
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