MolNFT v1 · #13739 · protein
A multi-generation analysis of cytochrome B562 redox variants: evolutionary strategies for modulating redox potential revealed using a library approach
1LM3 · Soluble cytochrome B562: “A multi-generation analysis of cytochrome B562 redox variants: evolutionary strategies for modulating redox…”. X-ray diffraction, 2 ligands (HEM, MG), 5 pockets (best druggability 0.68). MolNFT v1 #13739 on…
- PDB
- 1LM3
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEM, MG
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.68 | 0.85 | 23 | HEM |
| 2 | 198 | 0.68 | 0.85 | 23 | HEM |
| 3 | 135 | 0.38 | 0.73 | 24 | MG |
| 4 | 74 | 0.35 | 0.76 | 19 | empty |
| 5 | 53 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- B–D · 353 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1LM3 · A Multi-generation Analysis of Cytochrome b562 Redox Variants: Evolutionary Strategies… · the same entry in another collection · chain B against B, 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 0.97
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 1LM3 · PDBe 1LM3 · UniProt P0ABE7
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