Research workbench
Crystal structure of a ni-directed dimer of cytochrome CB562 with a quinolate-histidine hybrid coordination motif
Analyse Crystal structure of a ni-directed dimer of cytochrome CB562 with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L1M
- Type
- protein
- Length
- 106 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEM, HQI, NI
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble cytochrome B562 | protein | 106 | 80% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- HQI · N-(8-hydroxyquinolin-5-yl)acetamide · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.59 | 0.82 | 22 | HEM |
Modifications
Observed in the structure: 2 cofactor, 1 covalent (heme attachment, covalent ligand).
Compared structures
- 3L1M · Crystal Structure of a Ni-directed Dimer of Cytochrome cb562 with a Quinolate-Histidine… · the same entry in another collection · chain A against A, 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 0.97
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 3L1M · PDBe 3L1M · UniProt P0ABE7
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