MolNFT v1 · #12489 · protein
Cytochrome C6 from arthrospira maxima: an assembly of 24 subunits in the form of an oblate shell
1KIB: “Cytochrome C6 from arthrospira maxima: an assembly of 24 subunits in the form of an oblate shell”. X-ray diffraction, 1 ligand (HEC), 9 pockets (best druggability 0.80). MolNFT v1 #12489 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1KIB
- Type
- protein
- Length
- 712 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C6
- UniProt
- P00118
- Ligands
- HEC
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Cytochrome C6 | protein | 89 | 61% helix, 2% strand | P00118 |
Ligands and binding sites
- HEC · Heme C · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.80 | 0.81 | 128 | HEC |
| 2 | 282 | 0.71 | 0.85 | 37 | HEC |
| 3 | 254 | 0.71 | 0.85 | 34 | HEC |
| 4 | 386 | 0.71 | 0.82 | 56 | HEC |
| 5 | 234 | 0.70 | 0.86 | 26 | HEC |
Interfaces
13 interfaces between chains.
- A–G · 315 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 313 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 308 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 301 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 296 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (heme c attachment).
Compared structures
- 1KIB · cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in the form of an… · the same entry in another collection · chain H against H, TM-score 1.00
- P00118 · AlphaFold monomer V2.0 prediction for cytochrome C6 (P00118) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 P00118
- Elsewhere: RCSB PDB 1KIB · PDBe 1KIB · UniProt P00118
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