MolNFT v1 · #72911 · protein
Crystal structure of the phenanthroline-modified cytochrome CB562 variant, mbp-PHEN2
3NMI · Soluble cytochrome B562: “Crystal structure of the phenanthroline-modified cytochrome CB562 variant, mbp-PHEN2”. X-ray diffraction, 2 ligands (HEM, PXX), 9 pockets (best druggability 0.84). MolNFT v1 #72911 on GenesisL1: 3D…
- PDB
- 3NMI
- Type
- protein
- Length
- 636 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEM, PXX
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- PXX · N-1,10-phenanthrolin-5-ylacetamide · ligand · 6 copies · chains A, C, B, F, D, E
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.84 | 0.89 | 76 | HEM, ACT |
| 2 | 510 | 0.83 | 0.89 | 66 | HEM, ACT |
| 3 | 968 | 0.80 | 0.82 | 83 | PXX |
| 4 | 160 | 0.58 | 0.82 | 24 | HEM |
| 5 | 57 | 0.57 | 0.90 | 19 | empty |
Interfaces
9 interfaces between chains.
- D–E · 593 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 581 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 572 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 551 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 518 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 6 covalent (heme attachment, covalent ligand).
Compared structures
- 3NMI · Crystal structure of the phenanthroline-modified cytochrome cb562 variant, MBP-Phen2 · the same entry in another collection · chain F against F, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 3NMI · PDBe 3NMI · UniProt P0ABE7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.