Research workbench
Structure of stacked C2S2M2-type psii-lhcii supercomplex from pisum sativum
Analyse Structure of stacked C2S2M2-type psii-lhcii supercomplex from pisum sativum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XNL
- Type
- protein
- Length
- 9,364 residues
- Chains
- 56
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorophyll a-B binding protein 8, chloroplastic; Chlorophyll a-B binding protein…
- EC
- 1.10.3.9
- UniProt
- P27490, Q04918, P06585, Q9XQR6, P06004, P06006, P13554, Q9XQR3, P13555, D5MAJ8, P60147, P69529, P14226, P16059, Q7Y1T5, Q8HS25, Q8VYY1, Q32902
- Ligands
- CLA, CHL, LHG, LUT, BCR, XAT, NEX, LMG, DGD, SQD, PHO, PL9, OEX, BCT, HEM, FE2…
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 25 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, G, N, Y, 5, g, n, y | Chlorophyll a-B binding protein 8, chloroplastic | protein | 219 | 53% helix, 2% strand | P27490 |
| 2, 6 | Chlorophyll a-B binding protein 8, chloroplastic | protein | 218 | 49% helix, 3% strand | P27490 |
| 3, 7 | Chlorophyll a-B binding protein, chloroplastic | protein | 220 | 52% helix, 1% strand | Q04918 |
| 4, 8 | Light harvesting chlorophyll A/B-binding protein LHCB6, CP24 | protein | 197 | 45% helix, 0% strand | — |
| 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 | 46% helix, 11% strand | Q9XQR6 |
| C, c | Photosystem II CP43 reaction center protein | protein | 450 | 56% helix, 6% strand | P06004 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 341 | 62% helix, 4% strand | P06006 |
| E, e | Cytochrome B559 subunit alpha | protein | 75 | 57% helix, 1% strand | P13554 |
| F, f | Cytochrome B559 subunit beta, psbf | protein | 30 | 77% helix, 3% strand | — |
| H, h | Photosystem II reaction center protein H | protein | 60 | 52% helix, 7% strand | Q9XQR3 |
| I, i | Photosystem II reaction center protein I, psbi | protein | 34 | 65% helix, 0% strand | — |
| J, j | Photosystem II reaction center protein J | protein | 35 | 60% helix, 3% strand | P13555 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 65% 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, 45% strand | P14226 |
| P, p | Oxygen-evolving enhancer protein 2, chloroplastic | protein | 186 | 17% helix, 39% strand | P16059 |
| Q, q | Oxygen-evolving enhancer protein 3 | protein | 129 | 69% helix, 0% strand | Q7Y1T5 |
| R, r | Light harvesting chlorophyll A/B-binding protein LHCB4, CP29 | protein | 234 | 44% helix, 6% strand | — |
| S, s | Light harvesting chlorophyll A/B-binding protein LHCB5, CP26 | protein | 218 | 51% helix, 2% strand | — |
| 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 | 46% helix, 2% strand | — |
| X, x | Photosystem II reaction center protein X | protein | 39 | 77% helix, 0% strand | Q8VYY1 |
| Z, z | Photosystem II reaction center protein Z | protein | 62 | 81% helix, 0% strand | Q32902 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 216 copies · chains 1, 3, 2, 4, R, A, D, T, L, I, W, B, H, X, M, t, C, S, K, Z, G, N, 5, Y, 7, 6, 8, r, a, d, l, i, w, b, h, x, m, c, s, k, z, g, n, y
- CHL · Chlorophyll B · ligand · 98 copies · chains 1, 2, 3, 4, G, Y, N, S, R, B, r, 5, 6, 7, 8, g, y, n, s, b
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 36 copies · chains 1, 2, 3, 4, B, R, C, S, I, W, A, D, L, M, T, G, N, Z, Y, 5, 6, 7, 8, b, r, c, s, i, w, a, d, l, m, t, g, n, z, y
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 32 copies · chains 1, 2, 3, 4, G, N, R, S, Y, 5, 6, 7, 8, g, n, r, s, y
- BCR · Beta-carotene · ligand · 24 copies · chains 4, A, I, b, B, M, t, C, K, S, Z, J, D, F, H, X, T, 8, a, i, m, c, k, s, z, j, d, f, h, x
- 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 · 16 copies · chains 1, 2, 3, 4, G, Y, N, R, 5, 6, 7, 8, g, y, n, r
- 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 · 16 copies · chains 1, R, 2, 3, G, N, S, y, Y, r, 5, 6, 7, g, n, s
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 14 copies · chains A, C, I, W, b, B, D, L, M, R, J, K, F, S, Z, a, c, i, w, d, l, m, r, j, k, f, s, z
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains B, a, i, o, A, C, J, D, H, I, O, b, c, j, d, 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, K, T, b, h, B, L, l, m, t, M, a, c, d, k, 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, 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, D, a, d
- 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 | 865 | 0.84 | 0.86 | 97 | DGD |
| 2 | 841 | 0.84 | 0.86 | 90 | DGD |
| 3 | 831 | 0.83 | 0.85 | 102 | PL9, LHG |
| 4 | 800 | 0.83 | 0.86 | 99 | PL9, LHG |
| 5 | 968 | 0.83 | 0.84 | 80 | CLA, BCR |
Interfaces
174 interfaces between chains.
- a–d · 5396 Ų buried · 77 hydrogen bonds · protein-protein
- A–D · 5389 Ų buried · 77 hydrogen bonds · protein-protein
- A–C · 3275 Ų buried · 41 hydrogen bonds · protein-protein
- a–c · 3273 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 3083 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 5XNL · Structure of stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum · the same entry in another collection · chain E against E, 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 Q04918
- 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 Q9XQR3
- 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 P16059
- Every structure of UniProt Q7Y1T5
- Every structure of UniProt Q8HS25
- Every structure of UniProt Q8VYY1
- Every structure of UniProt Q32902
- Elsewhere: RCSB PDB 5XNL · PDBe 5XNL · UniProt P27490 · UniProt Q04918 · UniProt P06585 · UniProt Q9XQR6 · UniProt P06004 · UniProt P06006 · UniProt P13554 · UniProt Q9XQR3 · UniProt P13555 · UniProt D5MAJ8 · UniProt P60147 · UniProt P69529 · UniProt P14226 · UniProt P16059 · UniProt Q7Y1T5 · UniProt Q8HS25 · UniProt Q8VYY1 · UniProt Q32902
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