Research workbench
Crystal structure of photosystem II from an sqdg-deficient mutant of thermosynechococcus elongatus
Analyse Crystal structure of photosystem II from an sqdg-deficient mutant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZZN
- 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 1; Photosystem II CP47 reaction center protein; Photosystem II…
- EC
- 1.10.3.9
- UniProt
- P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, Q8DHA7, P0A431, Q8DIQ0, Q9F1L5, P0A386, Q8DJI1, Q9F1R6, Q8DHJ2
- Ligands
- CLA, UNL, BCR, LHG, LMG, DGD, PHO, PL9, OEX, BCT, HEM, RRX, HEC, CA, MG, FE2, CL
- 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 1 (EC 1.10.3.9) | protein | 334 | 60% helix, 4% strand | P0A444 |
| B | Photosystem II CP47 reaction center protein | protein | 505 | 50% helix, 11% strand | Q8DIQ1 |
| C | Photosystem II CP43 reaction center protein | protein | 451 | 58% helix, 6% strand | Q8DIF8 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 342 | 63% helix, 4% strand | Q8CM25 |
| E | Cytochrome B559 subunit alpha | protein | 80 | 55% helix, 0% strand | Q8DIP0 |
| F | Cytochrome B559 subunit beta | protein | 34 | 68% helix, 0% strand | Q8DIN9 |
| H, h | Photosystem II reaction center protein H | protein | 63 | 52% helix, 3% strand | Q8DJ43 |
| I | Photosystem II reaction center protein I | protein | 35 | 74% helix, 0% strand | Q8DJZ6 |
| J | Photosystem II reaction center protein J | protein | 37 | 62% helix, 0% strand | P59087 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 81% helix, 0% strand | Q9F1K9 |
| L | Photosystem II reaction center protein L | protein | 36 | 64% helix, 6% strand | Q8DIN8 |
| M | Photosystem II reaction center protein M | protein | 33 | 73% helix, 0% strand | Q8DHA7 |
| O, o | Photosystem II manganese-stabilizing polypeptide | protein | 243 | 6% helix, 47% strand | P0A431 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | Q8DIQ0 |
| U, u | Photosystem II 12 kda extrinsic protein | protein | 97 | 51% helix, 4% strand | Q9F1L5 |
| V, v | Cytochrome C-550 | protein | 137 | 48% helix, 6% strand | P0A386 |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 29 | 79% helix, 0% strand | Q8DJI1 |
| X | Photosystem II reaction center X protein | protein | 39 | 77% helix, 0% strand | Q9F1R6 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 85% helix, 0% strand | Q8DHJ2 |
| b | Photosystem II CP47 reaction center protein | protein | 504 | 50% helix, 11% strand | Q8DIQ1 |
| c | Photosystem II CP43 reaction center protein | protein | 455 | 57% helix, 6% strand | Q8DIF8 |
| e | Cytochrome B559 subunit alpha | protein | 81 | 54% helix, 0% strand | Q8DIP0 |
| f | Cytochrome B559 subunit beta | protein | 32 | 72% helix, 0% strand | Q8DIN9 |
| i | Photosystem II reaction center protein I | protein | 36 | 72% helix, 0% strand | Q8DJZ6 |
| j | Photosystem II reaction center protein J | protein | 40 | 58% helix, 0% strand | P59087 |
| l | Photosystem II reaction center protein L | protein | 35 | 66% helix, 6% strand | Q8DIN8 |
| m | Photosystem II reaction center protein M | protein | 34 | 71% helix, 0% strand | Q8DHA7 |
| x | Photosystem II reaction center X protein | protein | 38 | 79% helix, 0% strand | Q9F1R6 |
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, f, i, b, h, l, m, c, k, y, z, x
- UNL · Unknown ligand · ligand · 52 copies · chains A, b, C, D, J, K, T, B, H, X, m, t, E, F, I, Y, U, Z, a, i, d, h, x, M, c, k, z, e, j, y, f, u
- BCR · Beta-carotene · ligand · 20 copies · chains A, I, B, M, t, C, D, F, J, K, Z, T, b, Y, a, i, m, c, k, z, d, f, j, y
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 12 copies · chains A, B, D, L, M, T, C, E, F, X, a, b, d, l, m, t, c, e, f, x
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 10 copies · chains A, C, I, B, D, L, M, J, K, Y, Z, F, a, c, i, b, d, l, m, k, y, z, f, j
- 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
- 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 · 7 copies · chains B, O, F, V, b, c, o, f, v
- 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 · 5 copies · chains A, D, C, a, d, c, u, v
- DMS · Dimethyl sulfoxide · additive · 95 copies · chains A, b, D, O, E, B, U, M, H, L, a, C, V, I, F, i, o, d, e, h, u, l, m, c, v, t, f, j
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 22 copies · chains B, a, o, O, C, D, H, A, b, U, V, c, d, h, v
- LMT · Dodecyl-beta-D-maltoside · additive · 19 copies · chains A, D, M, O, b, B, H, X, C, I, E, F, J, l, m, L, T, Z, a, d, o, h, c, i, j, t, z
- GOL · Glycerol · additive · 5 copies · chains A, C, V, D, O, b, a, c, v, e, j
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 | 992 | 0.87 | 0.88 | 78 | CLA, BCR |
| 2 | 994 | 0.87 | 0.87 | 82 | CLA, BCR |
| 3 | 917 | 0.85 | 0.87 | 83 | DMS, HEC |
| 4 | 925 | 0.85 | 0.86 | 79 | DMS, HEC |
| 5 | 1161 | 0.82 | 0.83 | 100 | LHG, PL9 |
Interfaces
130 interfaces between chains.
- a–d · 5489 Ų buried · 66 hydrogen bonds · protein-protein
- A–D · 5486 Ų buried · 68 hydrogen bonds · protein-protein
- A–C · 3292 Ų buried · 39 hydrogen bonds · protein-protein
- a–c · 3275 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 3036 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 cofactor, 2 disulfide (formylation, heme c attachment, disulfide, nonstandard).
Compared structures
- 5ZZN · Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus… · 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 P0A444
- Every structure of UniProt Q8DIQ1
- Every structure of UniProt Q8DIF8
- Every structure of UniProt Q8CM25
- Every structure of UniProt Q8DIP0
- Every structure of UniProt Q8DIN9
- Every structure of UniProt Q8DJ43
- Every structure of UniProt Q8DJZ6
- Every structure of UniProt P59087
- Every structure of UniProt Q9F1K9
- Every structure of UniProt Q8DIN8
- Every structure of UniProt Q8DHA7
- Every structure of UniProt P0A431
- Every structure of UniProt Q8DIQ0
- Every structure of UniProt Q9F1L5
- Every structure of UniProt P0A386
- Every structure of UniProt Q8DJI1
- Every structure of UniProt Q9F1R6
- Every structure of UniProt Q8DHJ2
- Elsewhere: RCSB PDB 5ZZN · PDBe 5ZZN · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt Q8DIP0 · UniProt Q8DIN9 · UniProt Q8DJ43 · UniProt Q8DJZ6 · UniProt P59087 · UniProt Q9F1K9 · UniProt Q8DIN8 · UniProt Q8DHA7 · UniProt P0A431 · UniProt Q8DIQ0 · UniProt Q9F1L5 · UniProt P0A386 · UniProt Q8DJI1 · UniProt Q9F1R6 · UniProt Q8DHJ2
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