MolNFT v1 · #154768 · protein
Hyperthermophilic respiratory complex III
6KLS · Rieske-I iron sulfur protein: “Hyperthermophilic respiratory complex III”. Electron microscopy, 5 ligands (DLX, HEM, PGV), 20 pockets (best druggability 0.89). MolNFT v1 #154768 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6KLS
- Type
- protein
- Length
- 1,530 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rieske-I iron sulfur protein; Cytochrome B subunit; Cytochrome C
- UniProt
- O66460, O66458
- Ligands
- DLX, HEM, PGV, FES, HEC
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 48% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Rieske-I iron sulfur protein | protein | 134 | 18% helix, 19% strand | O66460 |
| B, E | Cytochrome B subunit | protein | 395 | 63% helix, 1% strand | — |
| C, F | Cytochrome C | protein | 236 | 42% helix, 5% strand | O66458 |
Ligands and binding sites
- DLX · 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15, 19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione · ligand · 6 copies · chains B, E, A, C, D, F
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains B, E
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 3 copies · chains B, C, E, F
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, D
- HEC · Heme C · ligand · 2 copies · chains B, C, D, A, E, 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 | 722 | 0.89 | 0.93 | 82 | HEM |
| 2 | 747 | 0.85 | 0.88 | 90 | HEC |
| 3 | 511 | 0.82 | 0.88 | 52 | HEM |
| 4 | 512 | 0.82 | 0.88 | 49 | HEM |
| 5 | 505 | 0.81 | 0.88 | 70 | empty |
Interfaces
14 interfaces between chains.
- E–F · 2485 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2472 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 1657 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 604 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 598 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 covalent, 2 disulfide (heme c attachment, covalent ligand, disulfide).
Compared structures
- 6KLS · Hyperthermophilic respiratory Complex III · 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 O66460
- Every structure of UniProt O66458
- Elsewhere: RCSB PDB 6KLS · PDBe 6KLS · UniProt O66460 · UniProt O66458
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