Research workbench
Crystal structure of N64DEL mutant of nitrosomonas europaea cytochrome C552 (monoclinic space group)
Analyse Crystal structure of N64DEL mutant of nitrosomonas europaea cytochrome C552… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZOX
- Type
- protein
- Length
- 320 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C-552
- EC
- 1.7.2.2
- UniProt
- P95339
- Ligands
- HEC
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome C-552 (EC 1.7.2.2) | protein | 80 | 46% helix, 3% strand | P95339 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.84 | 0.90 | 73 | HEC |
| 2 | 876 | 0.81 | 0.83 | 103 | HEC |
| 3 | 223 | 0.76 | 0.90 | 34 | HEC |
Interfaces
5 interfaces between chains.
- B–C · 547 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 534 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 319 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 215 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 202 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 3ZOX · Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (monoclinic… · the same entry in another collection · chain D against D, TM-score 1.00
- P95339 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P95339) · a predicted model of the same protein · chain B 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 P95339
- Elsewhere: RCSB PDB 3ZOX · PDBe 3ZOX · UniProt P95339
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