Research workbench
Crystal structure of mvfr ligand binding domain in complex with M64
Analyse Crystal structure of mvfr ligand binding domain in complex with M64 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B8A
- Type
- protein
- Length
- 405 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding transcriptional regulator
- UniProt
- A0A072ZLE6
- Ligands
- CZG, NCO
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-binding transcriptional regulator | protein | 203 | 33% helix, 28% strand | A0A072ZLE6 |
| B | DNA-binding transcriptional regulator | protein | 202 | 33% helix, 28% strand | A0A072ZLE6 |
Ligands and binding sites
- CZG · 2-[(5-nitro-1H-benzimidazol-2-yl)sulfanyl]-N-(4-phenoxyphenyl)acetamide · ligand · 2 copies · chains A, B
- NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.86 | 0.87 | 96 | CZG |
| 2 | 106 | 0.41 | 0.76 | 23 | empty |
| 3 | 56 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1279 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6B8A · Crystal structure of MvfR ligand binding domain in complex with M64 · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A072ZLE6
- Elsewhere: RCSB PDB 6B8A · PDBe 6B8A · UniProt A0A072ZLE6
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