MolNFT v1 · #142462 · protein
Crystal structure of dddk
6A53 · Novel protein with potential cupin domain: “Crystal structure of dddk”. X-ray diffraction, 1 ligand (MN), 3 pockets (best druggability 0.60). MolNFT v1 #142462 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6A53
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Novel protein with potential cupin domain
- UniProt
- Q4FNM4
- Ligands
- MN
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Novel protein with potential cupin domain | protein | 126 | 9% helix, 48% strand | Q4FNM4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.60 | 0.87 | 18 | empty |
| 2 | 55 | 0.56 | 0.89 | 14 | empty |
| 3 | 116 | 0.41 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1514 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6A53 · Crystal structure of DddK · the same entry in another collection · chain A against A, 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 Q4FNM4
- Elsewhere: RCSB PDB 6A53 · PDBe 6A53 · UniProt Q4FNM4
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