MolNFT v1 · #114203 · protein
Crystal structure analysis of photosystem II complex
5B5E · Photosystem II protein D1: “Crystal structure analysis of photosystem II complex”. X-ray diffraction, 18 ligands (CLA, UNL, BCR), 20 pockets (best druggability 0.87). MolNFT v1 #114203 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5B5E
- Type
- protein
- Length
- 5,253 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, UNL, BCR, LHG, LMG, DGD, SQD, PHO, PL9, OEX, BCT, HEM, RRX, HEC, CA, FE2…
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 28 distinct chains · 55% helix, 8% 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 | 505 | 49% 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 | Cytochrome B559 subunit alpha | protein | 81 | 53% helix, 0% strand | P12238 |
| F | Cytochrome B559 subunit beta | protein | 35 | 66% helix, 0% strand | P12239 |
| H, h | Photosystem II reaction center protein H | protein | 63 | 51% helix, 3% strand | P19052 |
| I | Photosystem II reaction center protein I | protein | 35 | 74% helix, 0% strand | P12240 |
| J | Photosystem II reaction center protein J | protein | 36 | 64% helix, 0% strand | Q7DGD4 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 81% helix, 0% strand | P19054 |
| 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 | P12312 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 243 | 6% helix, 47% strand | D0VWR2 |
| 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 | 48% 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 | 38 | 79% helix, 0% strand | D0VWR4 |
| Z | Photosystem II reaction center protein Z | protein | 62 | 87% helix, 0% strand | D0VWR5 |
| b | Photosystem II CP47 reaction center protein | protein | 501 | 50% helix, 11% strand | D0VWR1 |
| c | Photosystem II CP43 reaction center protein | protein | 455 | 57% helix, 6% strand | D0VWR7 |
| e | Cytochrome B559 subunit alpha | protein | 79 | 54% helix, 0% strand | P12238 |
| f | Cytochrome B559 subunit beta | protein | 32 | 72% helix, 0% strand | P12239 |
| i | Photosystem II reaction center protein I | protein | 38 | 68% helix, 0% strand | P12240 |
| j | Photosystem II reaction center protein J | protein | 40 | 58% helix, 0% strand | Q7DGD4 |
| l | Photosystem II reaction center protein L | protein | 36 | 64% helix, 3% strand | P12241 |
| t | Photosystem II reaction center protein T | protein | 31 | 68% helix, 0% strand | P12313 |
| z | Photosystem II reaction center protein Z | protein | 61 | 82% helix, 0% strand | D0VWR5 |
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 · 53 copies · chains A, I, B, H, C, D, X, E, F, J, K, M, T, U, Z, a, i, b, h, c, d, x, e, j, k, m, t, u, z
- BCR · Beta-carotene · ligand · 20 copies · chains A, I, B, M, t, C, K, Z, D, F, J, T, b, Y, a, i, m, c, k, z, d, f, j, y
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 14 copies · chains A, I, B, D, L, M, T, C, E, F, K, a, i, c, d, j, k, b, l, m, t, e, f
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains B, D, L, M, A, C, I, J, K, Y, Z, H, X, F, a, c, i, j, k, y, z, b, d, h, x, f, l, m
- 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
- 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, M, a, c, d, j, k, e, f, x
- 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, e, f
- 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
- CA · Calcium ion · metal · 5 copies · chains B, O, b, 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
- DMS · Dimethyl sulfoxide · additive · 112 copies · chains A, I, D, E, O, b, B, U, H, o, V, L, C, F, a, i, d, u, h, m, c, v, e, x, j, k, l, f
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 20 copies · chains B, a, o, O, C, D, H, X, A, b, V, c, d, h, x, v
- LMT · Dodecyl-beta-D-maltoside · additive · 16 copies · chains A, D, O, b, B, H, X, M, m, t, a, E, F, J, C, I, l, T, Z, d, o, c, i, h, e, f, 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 | 1015 | 0.87 | 0.88 | 79 | CLA, BCR |
| 2 | 1179 | 0.87 | 0.87 | 82 | CLA, BCR |
| 3 | 845 | 0.85 | 0.87 | 75 | DMS, HEC |
| 4 | 999 | 0.85 | 0.85 | 92 | DMS, HEC |
| 5 | 699 | 0.83 | 0.86 | 74 | LHG |
Interfaces
130 interfaces between chains.
- a–d · 5486 Ų buried · 65 hydrogen bonds · protein-protein
- A–D · 5484 Ų buried · 67 hydrogen bonds · protein-protein
- A–C · 3298 Ų buried · 40 hydrogen bonds · protein-protein
- a–c · 3296 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 3042 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 modified, 2 disulfide (heme c attachment, formylation, disulfide).
Compared structures
- 5B5E · Crystal structure analysis of Photosystem II complex · the same entry in another collection · chain K against K, 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 5B5E · PDBe 5B5E · 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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