MolNFT v1 · #72913 · protein
Crystal structure of a zinc mediated dimer for the phenanthroline- modified cytochrome CB562 variant, mbp-PHEN2
3NMK · Soluble cytochrome B562: “Crystal structure of a zinc mediated dimer for the phenanthroline- modified cytochrome CB562 variant…”. X-ray diffraction, 3 ligands (HEM, PXX, ZN), 9 pockets (best druggability 0.79). MolNFT v1 #72913 on…
- PDB
- 3NMK
- Type
- protein
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEM, PXX, ZN
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- PXX · N-1,10-phenanthrolin-5-ylacetamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.79 | 0.80 | 70 | PXX, ZN |
| 2 | 140 | 0.59 | 0.84 | 23 | HEM |
| 3 | 147 | 0.58 | 0.82 | 23 | HEM |
| 4 | 154 | 0.57 | 0.81 | 23 | HEM |
| 5 | 147 | 0.56 | 0.81 | 23 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 415 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 411 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 180 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 126 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 covalent (heme attachment, covalent ligand).
Compared structures
- 3NMK · Crystal structure of a zinc mediated dimer for the phenanthroline-modified cytochrome… · the same entry in another collection · chain D against D, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A 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 P0ABE7
- Elsewhere: RCSB PDB 3NMK · PDBe 3NMK · UniProt P0ABE7
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