MolNFT v1 · #155948 · protein
Cryo-EM structure of the air-oxidized photosynthetic alternative complex III from roseiflexus castenholzii
6LOD · MULTIHEME_CYTC domain-containing protein: “Cryo-EM structure of the air-oxidized photosynthetic alternative complex III from roseiflexus castenholzii”. Electron microscopy, 5 ligands (HEC, SF4, EL6), 20 pockets (best druggability…
- PDB
- 6LOD
- Type
- protein
- Length
- 2,329 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MULTIHEME_CYTC domain-containing protein; Fe-S-cluster-containing hydrogenase components…
- UniProt
- A7NJ87, A7NJ88, A7NJ89, A7NJ90, A7NJ91, A7NJ92
- Ligands
- HEC, SF4, EL6, ACE, F3S
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 6 distinct chains · 40% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MULTIHEME_CYTC domain-containing protein | protein | 218 | 33% helix, 2% strand | A7NJ87 |
| B | Fe-S-cluster-containing hydrogenase components 1-like protein | protein | 929 | 21% helix, 16% strand | A7NJ88 |
| C | Polysulphide reductase nrfd | protein | 456 | 68% helix, 0% strand | A7NJ89 |
| D | Uncharacterized protein actd | protein | 174 | 34% helix, 9% strand | A7NJ90 |
| E | Cytochrome C domain-containing protein | protein | 157 | 27% helix, 3% strand | A7NJ91 |
| F | Uncharacterized protein actf | protein | 395 | 66% helix, 0% strand | A7NJ92 |
Ligands and binding sites
- HEC · Heme C · ligand · 6 copies · chains A, E, B, C, D
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains B
- EL6 · [(2S)-2-octadecanoyloxypropyl] octadecanoate · ligand · 2 copies · chains B, C, A, E
- ACE · Acetyl group · ligand · chains A, B, E
- F3S · FE3-S4 cluster · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.91 | 0.94 | 154 | HEC |
| 2 | 378 | 0.86 | 0.95 | 46 | empty |
| 3 | 387 | 0.86 | 0.94 | 51 | empty |
| 4 | 595 | 0.84 | 0.89 | 59 | empty |
| 5 | 278 | 0.80 | 0.91 | 39 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2724 Ų buried · 24 hydrogen bonds · protein-protein
- B–E · 2629 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2377 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2084 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 1818 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 cofactor, 4 covalent (heme c attachment, covalent ligand).
Compared structures
- 6LOD · Cryo-EM structure of the air-oxidized photosynthetic alternative complex III from… · the same entry in another collection · chain A against A, 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 A7NJ87
- Every structure of UniProt A7NJ88
- Every structure of UniProt A7NJ89
- Every structure of UniProt A7NJ90
- Every structure of UniProt A7NJ91
- Every structure of UniProt A7NJ92
- Elsewhere: RCSB PDB 6LOD · PDBe 6LOD · UniProt A7NJ87 · UniProt A7NJ88 · UniProt A7NJ89 · UniProt A7NJ90 · UniProt A7NJ91 · UniProt A7NJ92
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