MolNFT v1 · #50293 · protein
High resolution crystal structure of the escherichia COLI cytochrome C nitrite reductase.
2RDZ · Cytochrome C-552: “High resolution crystal structure of the escherichia COLI cytochrome C nitrite reductase.”. X-ray diffraction, 3 ligands (HEC, CA, SO4), 20 pockets (best druggability 0.88). MolNFT v1 #50293 on GenesisL1: 3D…
- PDB
- 2RDZ
- Type
- protein
- Length
- 1,764 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
- P0ABK9
- Ligands
- HEC, CA, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome C-552 (EC 1.7.2.2) | protein | 441 | 57% helix, 5% strand | P0ABK9 |
Ligands and binding sites
- HEC · Heme C · ligand · 20 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.88 | 0.93 | 94 | HEC |
| 2 | 525 | 0.87 | 0.93 | 87 | HEC |
| 3 | 440 | 0.83 | 0.91 | 59 | HEC |
| 4 | 286 | 0.82 | 0.93 | 39 | HEC |
| 5 | 218 | 0.78 | 0.92 | 45 | EDO, HEC |
Interfaces
4 interfaces between chains.
- A–B · 1546 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1527 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 401 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 73 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 39 cofactor (heme c attachment).
Compared structures
- 2RDZ · High Resolution Crystal Structure of the Escherichia coli Cytochrome c Nitrite Reductase. · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABK9 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P0ABK9) · a predicted model of the same protein · 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 P0ABK9
- Elsewhere: RCSB PDB 2RDZ · PDBe 2RDZ · UniProt P0ABK9
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