Research workbench
Psii-lhcii C2S2 supercomplex from pisum sativum grown in high light conditions
Analyse Psii-lhcii C2S2 supercomplex from pisum sativum grown in high light conditions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YP7
- Type
- protein
- Length
- 7,002 residues
- Chains
- 44
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorophyll a-B binding protein 8, chloroplastic; Photosystem II protein D1; Photosystem…
- EC
- 1.10.3.9
- UniProt
- P27490, P06585, Q9XQR6, P06004, P06006, P13554, P62096, Q9XQR3, D5MAJ9, P13555, D5MAJ8, P60147, P69529, P14226, Q8HS25, A0A2D0TCJ2, Q8VYY1, Q32902
- Ligands
- CLA, CHL, LHG, BCR, LMG, LUT, DGD, XAT, SQD, NEX, PHO, PL9, OEX, BCT, HEM, FE2…
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 20 distinct chains · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| g, n, y, G, N, Y | Chlorophyll a-B binding protein 8, chloroplastic | protein | 219 | 56% helix, 1% strand | P27490 |
| a, A | Photosystem II protein D1 (EC 1.10.3.9) | protein | 334 | 57% helix, 4% strand | P06585 |
| b, B | Photosystem II CP47 reaction center protein | protein | 503 | 47% helix, 10% strand | Q9XQR6 |
| c, C | Photosystem II CP43 reaction center protein | protein | 450 | 55% helix, 5% strand | P06004 |
| d, D | Photosystem II D2 protein (EC 1.10.3.9) | protein | 341 | 62% helix, 2% strand | P06006 |
| e, E | Cytochrome B559 subunit alpha | protein | 75 | 60% helix, 0% strand | P13554 |
| f, F | Cytochrome B559 subunit beta | protein | 30 | 80% helix, 0% strand | P62096 |
| h, H | Photosystem II reaction center protein H | protein | 60 | 53% helix, 5% strand | Q9XQR3 |
| i, I | Photosystem II reaction center protein I | protein | 34 | 68% helix, 0% strand | D5MAJ9 |
| j, J | Photosystem II reaction center protein J | protein | 35 | 63% helix, 0% strand | P13555 |
| k, K | Photosystem II reaction center protein K | protein | 37 | 76% helix, 0% strand | D5MAJ8 |
| l, L | Photosystem II reaction center protein L | protein | 37 | 62% helix, 3% strand | P60147 |
| m, M | Photosystem II reaction center protein M | protein | 33 | 82% helix, 0% strand | P69529 |
| o, O | Oxygen-evolving enhancer protein 1, chloroplastic | protein | 248 | 9% helix, 42% strand | P14226 |
| t, T | Photosystem II reaction center protein T | protein | 32 | 66% helix, 0% strand | Q8HS25 |
| w, W | Photosystem II reaction center protein W | protein | 54 | 48% helix, 0% strand | A0A2D0TCJ2 |
| x, X | Ultraviolet-B-repressible protein | protein | 39 | 77% helix, 0% strand | Q8VYY1 |
| z, Z | Photosystem II reaction center protein Z | protein | 62 | 87% helix, 0% strand | Q32902 |
| r, R | Light harvesting chlorophyll A/B-binding protein LHCB4.3 | protein | 222 | 48% helix, 4% strand | — |
| s, S | Light harvesting chlorophyll A/B-binding protein LHCB5, CP26 | protein | 218 | 46% helix, 1% strand | — |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 150 copies · chains g, y, n, w, G, Y, N, W, a, d, i, b, h, l, m, c, s, k, z, x, A, D, I, B, X, H, L, M, C, S, K, Z, r, R
- CHL · Chlorophyll B · ligand · 48 copies · chains g, y, n, s, R, G, Y, N, S, r
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 26 copies · chains g, n, y, G, N, Y, b, r, c, s, w, a, d, l, t, m, B, C, S, W, A, D, L, T, M, R
- BCR · Beta-carotene · ligand · 22 copies · chains a, i, b, m, T, c, k, z, s, d, f, j, h, x, A, I, t, B, M, C, Z, S, D, F, J, H, X, K
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 14 copies · chains b, r, c, z, s, d, f, j, k, a, i, w, B, R, A, C, I, W, Z, S, D, F, J, K, t, L, M, l, m, T
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 12 copies · chains g, n, y, G, N, Y, r, R
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains a, o, B, c, j, d, b, h, A, O, C, J, D, H
- XAT · (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol · ligand · 8 copies · chains g, y, n, G, Y, N, r, R
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 8 copies · chains a, B, c, d, k, l, m, M, t, b, A, T, C, D, K, L
- NEX · (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R, 6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13, 15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol · ligand · 7 copies · chains g, n, y, R, N, Y, r
- 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, l, t, A, D, 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
- FE2 · Fe (II) ion · metal · 2 copies · chains a, A
- CL · Chloride ion · ion · 4 copies · chains a, d, c, A, D, C
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 | 677 | 0.86 | 0.90 | 88 | empty |
| 2 | 696 | 0.85 | 0.89 | 104 | empty |
| 3 | 570 | 0.85 | 0.90 | 74 | empty |
| 4 | 717 | 0.85 | 0.88 | 90 | empty |
| 5 | 324 | 0.85 | 0.94 | 49 | OEX, CL |
Interfaces
132 interfaces between chains.
- A–D · 5167 Ų buried · 46 hydrogen bonds · protein-protein
- a–d · 5141 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2927 Ų buried · 22 hydrogen bonds · protein-protein
- a–c · 2891 Ų buried · 20 hydrogen bonds · protein-protein
- b–d · 2820 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 85 covalent, 2 cofactor (covalent ligand, heme attachment).
Compared structures
- 6YP7 · PSII-LHCII C2S2 supercomplex from Pisum sativum grown in high light conditions · the same entry in another collection · chain y against y, 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 P27490
- Every structure of UniProt P06585
- Every structure of UniProt Q9XQR6
- Every structure of UniProt P06004
- Every structure of UniProt P06006
- Every structure of UniProt P13554
- Every structure of UniProt P62096
- Every structure of UniProt Q9XQR3
- Every structure of UniProt D5MAJ9
- Every structure of UniProt P13555
- Every structure of UniProt D5MAJ8
- Every structure of UniProt P60147
- Every structure of UniProt P69529
- Every structure of UniProt P14226
- Every structure of UniProt Q8HS25
- Every structure of UniProt A0A2D0TCJ2
- Every structure of UniProt Q8VYY1
- Every structure of UniProt Q32902
- Elsewhere: RCSB PDB 6YP7 · PDBe 6YP7 · UniProt P27490 · UniProt P06585 · UniProt Q9XQR6 · UniProt P06004 · UniProt P06006 · UniProt P13554 · UniProt P62096 · UniProt Q9XQR3 · UniProt D5MAJ9 · UniProt P13555 · UniProt D5MAJ8 · UniProt P60147 · UniProt P69529 · UniProt P14226 · UniProt Q8HS25 · UniProt A0A2D0TCJ2 · UniProt Q8VYY1 · UniProt Q32902
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.