MolNFT v1 · #72912 · protein
Crystal structure of a nickel mediated dimer for the phenanthroline- modified cytochrome CB562 variant, mbp-PHEN2
3NMJ · Soluble cytochrome B562: “Crystal structure of a nickel mediated dimer for the phenanthroline- modified cytochrome CB562 variant…”. X-ray diffraction, 3 ligands (HEM, PXX, NI), 11 pockets (best druggability 0.80). MolNFT v1 #72912…
- PDB
- 3NMJ
- Type
- protein
- Length
- 423 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEM, PXX, NI
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
| B | Soluble cytochrome B562 | protein | 105 | 81% 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
- NI · Nickel (II) ion · metal · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.80 | 0.81 | 55 | PXX, NI |
| 2 | 150 | 0.60 | 0.83 | 23 | HEM |
| 3 | 145 | 0.58 | 0.82 | 23 | HEM |
| 4 | 90 | 0.56 | 0.85 | 17 | HEM |
| 5 | 77 | 0.54 | 0.86 | 15 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 414 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 411 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 219 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 135 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 134 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 covalent (heme attachment, covalent ligand).
Compared structures
- 3NMJ · Crystal structure of a nickel 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 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 P0ABE7
- Elsewhere: RCSB PDB 3NMJ · PDBe 3NMJ · UniProt P0ABE7
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