Research workbench
Reaction centre light harvesting complex 1 from blc. virids
Analyse Reaction centre light harvesting complex 1 from blc. virids in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ET5
- Type
- protein
- Length
- 3,491 residues
- Chains
- 54
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center cytochrome C subunit; Reaction center protein L chain…
- UniProt
- P07173, P06009, P06010, P06008, P04123, P04124, P04126
- Ligands
- BCB, NS0, HEM, BPB, UQ9, MQ9, NS5, FE, SO4
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 7 distinct chains · 49% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Photosynthetic reaction center cytochrome C subunit | protein | 332 | 42% helix, 4% strand | P07173 |
| L | Reaction center protein L chain | protein | 273 | 66% helix, 4% strand | P06009 |
| M | Reaction center protein M chain | protein | 323 | 62% helix, 4% strand | P06010 |
| H | Reaction center protein H chain | protein | 258 | 24% helix, 24% strand | P06008 |
| z, F, K, P, S, V, Y, b, e, h, k, n, q, t, w, 3, 6 | Light-harvesting protein B-1015 alpha chain | protein | 58 | 53% helix, 0% strand | P04123 |
| 1, G, N, Q, T, W, Z, c, f, i, l, o, r, u, x, 4, 7 | Light-harvesting protein B-1015 beta chain | protein | 55 | 45% helix, 0% strand | P04124 |
| 2, I, O, R, U, X, a, d, g, j, m, p, s, v, y, 5 | Light-harvesting protein B-1015 gamma chain | protein | 24 | 67% helix, 0% strand | P04126 |
Ligands and binding sites
- BCB · Bacteriochlorophyll B · ligand · 38 copies · chains L, M, z, 1, 2, 3, 4, w, x, y, F, K, G, N, I, P, Q, O, S, T, R, V, W, U, Y, Z, X, b, c, a, e, f, d, h, i, g, k, l, j, n, o, m, q, r, p, t, u, s, H, v, 6, 7, 5
- NS0 · all-trans-1,2-dihydroneurosporene · ligand · 17 copies · chains z, 1, 2, w, 3, F, K, 6, G, I, P, N, O, S, Q, R, V, T, U, Y, W, X, b, Z, a, e, c, d, h, f, g, k, i, j, n, l, m, q, o, p, t, r, s, u, v, x, y, 4, 5, 7
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, L, M
- BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
- UQ9 · Ubiquinone-9 · ligand · 2 copies · chains L, M, 3, 6
- MQ9 · Menaquinone-9 · ligand · chains L, M, H, z, 3
- NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains M, h, k
- FE · Fe (III) ion · metal · chains L, M
- SO4 · Sulfate ion · ion · 7 copies · chains L, M, H, k
- LDA · Lauryl dimethylamine-N-oxide · additive · 2 copies · chains L, M, H
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 | 1067 | 0.89 | 0.90 | 114 | HEM |
| 2 | 999 | 0.83 | 0.84 | 102 | NS5 |
| 3 | 818 | 0.83 | 0.85 | 78 | BCB |
| 4 | 604 | 0.81 | 0.86 | 68 | SO4 |
| 5 | 601 | 0.81 | 0.86 | 72 | empty |
Interfaces
189 interfaces between chains.
- L–M · 4386 Ų buried · 49 hydrogen bonds · protein-protein
- M–H · 2855 Ų buried · 41 hydrogen bonds · protein-protein
- C–M · 2725 Ų buried · 28 hydrogen bonds · protein-protein
- L–H · 1881 Ų buried · 19 hydrogen bonds · protein-protein
- C–L · 1766 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 cofactor, 1 modified (covalent ligand, heme attachment, formylation).
Compared structures
- 6ET5 · Reaction centre light harvesting complex 1 from Blc. virids · 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 P07173
- Every structure of UniProt P06009
- Every structure of UniProt P06010
- Every structure of UniProt P06008
- Every structure of UniProt P04123
- Every structure of UniProt P04124
- Every structure of UniProt P04126
- Elsewhere: RCSB PDB 6ET5 · PDBe 6ET5 · UniProt P07173 · UniProt P06009 · UniProt P06010 · UniProt P06008 · UniProt P04123 · UniProt P04124 · UniProt P04126
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