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Structural insights into a dimeric PSB27-photosystem II complex from a cyanobacterium thermosynechococcus vulcanus
Analyse Structural insights into a dimeric PSB27-photosystem II complex from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CZL
- Type
- protein
- Length
- 4,304 residues
- Chains
- 32
- Method
- electron microscopy
- 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, P19054, P12241, P12312, P12313, D0VWR5, D0VWR3, D0VWR4
- Ligands
- CLA, BCR, MGE, DGD, SQD, PHO, PQ9, LHG, BCT, HEM, CA, FE2, CL
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 19 distinct chains · 57% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem II protein D1 (EC 1.10.3.9) | protein | 324 | 57% helix, 3% strand | P51765 |
| B, b | Photosystem II CP47 reaction center protein | protein | 484 | 48% helix, 8% strand | D0VWR1 |
| C, c | Photosystem II CP43 reaction center protein | protein | 446 | 54% helix, 2% strand | D0VWR7 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 339 | 56% helix, 0% strand | D0VWR8 |
| E, e | Cytochrome B559 subunit alpha | protein | 65 | 52% helix, 0% strand | P12238 |
| F | Cytochrome B559 subunit beta | protein | 31 | 71% helix, 0% strand | P12239 |
| H, h | Photosystem II reaction center protein H | protein | 62 | 44% helix, 2% strand | P19052 |
| I, i | Photosystem II reaction center protein I | protein | 34 | 68% helix, 0% strand | P12240 |
| K | Photosystem II reaction center protein K | protein | 37 | 57% helix, 0% strand | P19054 |
| L, l | Photosystem II reaction center protein L | protein | 37 | 62% helix, 3% strand | P12241 |
| M, m | Photosystem II reaction center protein M | protein | 33 | 76% helix, 0% strand | P12312 |
| T, t | Photosystem II reaction center protein T | protein | 30 | 70% helix, 0% strand | P12313 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 87% helix, 0% strand | D0VWR5 |
| a | Photosystem II protein D1 (EC 1.10.3.9) | protein | 322 | 58% helix, 2% strand | P51765 |
| f | Cytochrome B559 subunit beta | protein | 28 | 86% helix, 0% strand | P12239 |
| k | Photosystem II reaction center protein K | protein | 34 | 62% helix, 0% strand | P19054 |
| Y, y | Photosystem II reaction center protein YCF12 | protein | 29 | 72% helix, 0% strand | D0VWR3 |
| n, N | PSB27 | protein | 108 | 69% helix, 0% strand | — |
| X, x | Photosystem II reaction center protein X | protein | 35 | 86% helix, 0% strand | D0VWR4 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, L, I, B, H, M, C, K, Z, Y, X, a, d, t, l, i, b, h, m, c, k, x, z, y
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, K, Z, D, F, H, T, b, a, i, m, c, k, z, d, f, h, x, y, Y
- MGE · (1S)-2-(alpha-L-allopyranosyloxy)-1-[(tridecanoyloxy) methyl]ethyl palmitate · ligand · 14 copies · chains A, B, D, L, M, C, I, F, T, b, m, a, c, i, d, f, l, t
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 8 copies · chains A, C, B, D, H, a, c, d, b, h
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 6 copies · chains A, T, b, C, D, K, L, M, l, B, H, a, t, c, d, k, m
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- PQ9 · 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18,22,26-heptaenyl]-2,3-dimethylbenzo-1,4-quinone · ligand · 4 copies · chains A, D, F, L, T, a, d, l, t
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains A, C, D, a, c, d
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, e, f
- CA · Calcium ion · metal · 2 copies · chains C, c
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 2 copies · chains n, N
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, b, B, a, t, M, T, m
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 | 805 | 0.85 | 0.87 | 77 | CLA, BCR |
| 2 | 960 | 0.83 | 0.84 | 68 | BCR, CLA |
| 3 | 906 | 0.83 | 0.85 | 111 | DGD |
| 4 | 1140 | 0.83 | 0.84 | 115 | empty |
| 5 | 1096 | 0.83 | 0.84 | 115 | empty |
Interfaces
81 interfaces between chains.
- a–d · 5152 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 4987 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 2545 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 2521 Ų buried · 25 hydrogen bonds · protein-protein
- b–d · 2519 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 covalent (covalent ligand, additive adduct).
Compared structures
- 7CZL · Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium… · the same entry in another collection · chain I against I, 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 P19054
- Every structure of UniProt P12241
- Every structure of UniProt P12312
- Every structure of UniProt P12313
- Every structure of UniProt D0VWR5
- Every structure of UniProt D0VWR3
- Every structure of UniProt D0VWR4
- Elsewhere: RCSB PDB 7CZL · PDBe 7CZL · UniProt P51765 · UniProt D0VWR1 · UniProt D0VWR7 · UniProt D0VWR8 · UniProt P12238 · UniProt P12239 · UniProt P19052 · UniProt P12240 · UniProt P19054 · UniProt P12241 · UniProt P12312 · UniProt P12313 · UniProt D0VWR5 · UniProt D0VWR3 · UniProt D0VWR4
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