MolNFT v1 · #84575 · protein
Crystal structure of N64DEL mutant of nitrosomonas europaea cytochrome C552 (monoclinic space group)
3ZOX · Cytochrome C-552: “Crystal structure of N64DEL mutant of nitrosomonas europaea cytochrome C552 (monoclinic space group)”. X-ray diffraction, 1 ligand (HEC), 3 pockets (best druggability 0.84). MolNFT v1 #84575 on GenesisL1: 3D…
- 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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