MolNFT v1 · #139363 · protein
HIS/DOPA ligated cytochrome C from an anammox organism ksu-1
5XDH · Putative cytochrome C: “HIS/DOPA ligated cytochrome C from an anammox organism ksu-1”. X-ray diffraction, 2 ligands (HEC, SO4), 3 pockets (best druggability 0.88). MolNFT v1 #139363 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XDH
- Type
- protein
- Length
- 343 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cytochrome C
- UniProt
- I3IL56
- Ligands
- HEC, SO4
- Pockets
- 3 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Putative cytochrome C | protein | 86 | 53% helix, 0% strand | I3IL56 |
| C | Putative cytochrome C | protein | 85 | 59% helix, 0% strand | I3IL56 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.88 | 0.89 | 126 | HEC |
| 2 | 105 | 0.36 | 0.74 | 22 | empty |
| 3 | 50 | 0.24 | 0.73 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 597 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 547 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 317 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 316 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 4 modified (heme c attachment, nonstandard).
Compared structures
- 5XDH · His/DOPA ligated cytochrome c from an anammox organism KSU-1 · 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 I3IL56
- Elsewhere: RCSB PDB 5XDH · PDBe 5XDH · UniProt I3IL56
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