Research workbench
Rc-LH1(14)-W complex from rhodopseudomonas palustris
Analyse Rc-LH1(14)-W complex from rhodopseudomonas palustris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z5S
- Type
- protein
- Length
- 2,214 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light harvesting complex 1 protein W; Reaction center protein M chain; Reaction center…
- UniProt
- Q6N1K3, A0A4Z7, O83005, A0A4Z9, Q6N9L4, Q6N9L5
- Ligands
- BCL, CRT, CDL, U10, 6PL, BPH, QAK, PGT, FE
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 11 distinct chains · 57% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W | Light harvesting complex 1 protein W | protein | 94 | 63% helix, 0% strand | Q6N1K3 |
| M | Reaction center protein M chain | protein | 299 | 65% helix, 2% strand | A0A4Z7 |
| L | Reaction center protein L chain | protein | 276 | 63% helix, 4% strand | O83005 |
| H | H subunit of photosynthetic reaction center complex | protein | 251 | 25% helix, 20% strand | A0A4Z9 |
| 1, 5, 3, Y, V, T, C, R, P, N, G, E | Light-harvesting complex 1 alpha chain | protein | 46 | 61% helix, 0% strand | Q6N9L4 |
| 2, Z, X, U, B, K, I | Light-harvesting complex 1 beta chain | protein | 47 | 64% helix, 4% strand | Q6N9L5 |
| 6 | Light-harvesting complex 1 beta chain | protein | 42 | 76% helix, 0% strand | Q6N9L5 |
| 4 | Light-harvesting complex 1 beta chain | protein | 46 | 70% helix, 0% strand | Q6N9L5 |
| A | Light-harvesting complex 1 alpha chain | protein | 40 | 58% helix, 0% strand | Q6N9L4 |
| D, S, Q, O, F | Light-harvesting complex 1 beta chain | protein | 48 | 67% helix, 4% strand | Q6N9L5 |
| J | Light-harvesting complex 1 alpha chain | protein | 45 | 64% helix, 0% strand | Q6N9L4 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 32 copies · chains M, L, 1, 2, Y, Z, 3, 4, 5, 6, V, X, T, U, R, S, W, A, B, C, D, E, F, P, Q, N, O, J, K, G, I
- CRT · Spirilloxanthin · ligand · 13 copies · chains 1, 2, 3, Y, Z, 5, 4, V, X, T, W, A, B, C, D, E, U, R, S, P, Q, N, O, J, K, G, I, F
- CDL · Cardiolipin · ligand · 6 copies · chains M, L, H, P, N, C, G, E, 5, 3, J, F
- U10 · Ubiquinone-10 · ligand · 3 copies · chains M, L, H, C, 1, Y
- 6PL · (4S,7R)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 3 copies · chains M, H, N, L, C, E
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains M, L
- QAK · (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S}, 28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol · ligand · chains M, T, R
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains M, P, N
- FE · Fe (III) ion · metal · chains M, L
- LMT · Dodecyl-beta-D-maltoside · additive · 29 copies · chains M, P, W, L, A, 2, Z, 6, 4, X, U, B, D, R, S, Q, O, H, N, J, K, I, F
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 | 988 | 0.84 | 0.85 | 98 | CRT |
| 2 | 1170 | 0.82 | 0.83 | 90 | BCL, BPH |
| 3 | 1001 | 0.81 | 0.81 | 70 | BCL, LMT, CRT |
| 4 | 915 | 0.80 | 0.82 | 90 | 6PL, CRT |
| 5 | 107 | 0.78 | 0.97 | 34 | empty |
Interfaces
103 interfaces between chains.
- M–L · 4351 Ų buried · 51 hydrogen bonds · protein-protein
- M–H · 2860 Ų buried · 42 hydrogen bonds · protein-protein
- L–H · 1522 Ų buried · 12 hydrogen bonds · protein-protein
- 3–4 · 886 Ų buried · 7 hydrogen bonds · protein-protein
- G–I · 818 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (formylation).
Compared structures
- 6Z5S · RC-LH1(14)-W complex from Rhodopseudomonas palustris · the same entry in another collection · chain W against W, 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 Q6N1K3
- Every structure of UniProt A0A4Z7
- Every structure of UniProt O83005
- Every structure of UniProt A0A4Z9
- Every structure of UniProt Q6N9L4
- Every structure of UniProt Q6N9L5
- Elsewhere: RCSB PDB 6Z5S · PDBe 6Z5S · UniProt Q6N1K3 · UniProt A0A4Z7 · UniProt O83005 · UniProt A0A4Z9 · UniProt Q6N9L4 · UniProt Q6N9L5
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