Research workbench
Hyperthermophilic respiratory complex III
Analyse Hyperthermophilic respiratory complex III in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KLV
- 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; Cytochrome C
- UniProt
- O66460, O66458
- Ligands
- DLX, HEM, PGV, FES, AMY, HEC
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 49% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Rieske-I iron sulfur protein | protein | 134 | 17% helix, 8% strand | O66460 |
| B, E | Cytochrome B | protein | 395 | 63% helix, 1% strand | — |
| C, F | Cytochrome C | protein | 236 | 44% helix, 6% 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 · 4 copies · chains A, B, C, E, 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
- AMY · Antimycin · ligand · 2 copies · chains B, E
- 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 | 961 | 0.87 | 0.89 | 117 | HEC |
| 2 | 690 | 0.85 | 0.88 | 97 | HEC |
| 3 | 354 | 0.84 | 0.93 | 43 | HEM |
| 4 | 344 | 0.84 | 0.93 | 41 | HEM |
| 5 | 514 | 0.81 | 0.87 | 57 | HEM, AMY |
Interfaces
14 interfaces between chains.
- B–C · 2460 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 2452 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 1677 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 597 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 580 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 covalent, 2 disulfide (heme c attachment, covalent ligand, disulfide).
Compared structures
- 6KLV · 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 6KLV · PDBe 6KLV · UniProt O66460 · UniProt O66458
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