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Crystal structure of wild type nitrosomonas europaea cytochrome C552
Analyse Crystal structure of wild type 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
- 3ZOW
- Type
- protein
- Length
- 1,449 residues
- Chains
- 18
- 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
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, Q, R | Cytochrome C-552 (EC 1.7.2.2) | protein | 81 | 52% helix, 2% strand | P95339 |
| P | Cytochrome C-552 (EC 1.7.2.2) | protein | 72 | 42% helix, 6% strand | P95339 |
Ligands and binding sites
- HEC · Heme C · ligand · 18 copies · chains A, B, K, C, D, E, F, J, G, H, I, L, M, O, N, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.88 | 0.89 | 144 | HEC |
| 2 | 1000 | 0.88 | 0.89 | 123 | HEC |
| 3 | 547 | 0.82 | 0.88 | 81 | HEC |
| 4 | 780 | 0.82 | 0.85 | 99 | HEC |
| 5 | 308 | 0.79 | 0.90 | 55 | HEC |
Interfaces
35 interfaces between chains.
- A–J · 489 Ų buried · 6 hydrogen bonds · protein-protein
- Q–R · 481 Ų buried · 2 hydrogen bonds · protein-protein
- M–O · 470 Ų buried · 1 hydrogen bond · protein-protein
- J–R · 359 Ų buried · 0 hydrogen bonds · protein-protein
- L–P · 339 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 cofactor (heme c attachment).
Compared structures
- 3ZOW · Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 · the same entry in another collection · chain K against K, 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 P95339
- Elsewhere: RCSB PDB 3ZOW · PDBe 3ZOW · UniProt P95339
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