MolNFT v1 · #139702 · protein
Structure of unstacked C2S2M2-type psii-lhcii supercomplex from pisum sativum
5XNM · Chlorophyll a-B binding protein 8, chloroplastic: “Structure of unstacked C2S2M2-type psii-lhcii supercomplex from pisum sativum”. Electron microscopy, 16 ligands (CLA, CHL, LHG), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5XNM
- Type
- protein
- Length
- 8,712 residues
- Chains
- 54
- 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, 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 · 24 distinct chains · 51% helix, 7% 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 | 52% helix, 2% strand | P27490 |
| 2, 6 | Chlorophyll a-B binding protein 8, chloroplastic | protein | 218 | 50% helix, 2% 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 | 47% helix, 0% strand | — |
| A, a | Photosystem II protein D1 (EC 1.10.3.9) | protein | 334 | 56% helix, 5% 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 | 55% helix, 5% strand | P06004 |
| D, d | Photosystem II D2 protein (EC 1.10.3.9) | protein | 340 | 60% helix, 3% 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, 0% 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 | 34 | 62% helix, 3% strand | P13555 |
| K, k | Photosystem II reaction center protein K | protein | 37 | 68% 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 | 214 | 6% helix, 49% strand | P14226 |
| R, r | Light harvesting chlorophyll A/B-binding protein LHCB4, CP29 | protein | 234 | 47% 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 |
| U, u | Photosystem II luminal extrinsic protein tn, psbtn | protein | 25 | 64% helix, 0% strand | — |
| W, w | Photosystem II reaction center protein W, psbw | 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, M, t, C, S, K, Z, X, G, N, 5, Y, 7, 6, 8, r, a, d, l, i, w, b, h, m, c, s, k, z, x, 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, J, K, F, S, Z, a, c, i, w, d, l, m, j, k, f, s, z
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains B, a, i, o, A, C, J, D, H, U, I, O, b, c, j, d, h, u
- 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
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 | 911 | 0.84 | 0.85 | 109 | CLA, DGD |
| 2 | 1008 | 0.84 | 0.84 | 101 | CLA, LMG, DGD |
| 3 | 1098 | 0.83 | 0.84 | 90 | CLA, DGD |
| 4 | 1025 | 0.83 | 0.83 | 80 | CLA, BCR |
| 5 | 851 | 0.83 | 0.84 | 76 | CLA |
Interfaces
160 interfaces between chains.
- A–D · 5386 Ų buried · 67 hydrogen bonds · protein-protein
- a–d · 5382 Ų buried · 67 hydrogen bonds · protein-protein
- A–C · 3240 Ų buried · 31 hydrogen bonds · protein-protein
- a–c · 3232 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 3014 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5XNM · Structure of unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum · the same entry in another collection · chain F against F, 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 Q8HS25
- Every structure of UniProt Q8VYY1
- Every structure of UniProt Q32902
- Elsewhere: RCSB PDB 5XNM · PDBe 5XNM · 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 Q8HS25 · UniProt Q8VYY1 · UniProt Q32902
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