Research workbench
Crystal structure of cupin 2 conserved barrel domain protein from kribbella flavida dsm 17836
Analyse Crystal structure of cupin 2 conserved barrel domain protein from kribbella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J7M
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cupin 2 conserved barrel domain protein
- UniProt
- D2Q1L0
- Ligands
- NI
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cupin 2 conserved barrel domain protein | protein | 122 | 11% helix, 45% strand | D2Q1L0 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- EOH · Ethanol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.51 | 0.80 | 21 | EOH, PEG |
| 2 | 117 | 0.50 | 0.80 | 17 | EOH, PEG |
| 3 | 125 | 0.50 | 0.80 | 23 | empty |
| 4 | 98 | 0.47 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1909 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 5J7M · Crystal structure of Cupin 2 conserved barrel domain protein from Kribbella flavida DSM… · 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 D2Q1L0
- Elsewhere: RCSB PDB 5J7M · PDBe 5J7M · UniProt D2Q1L0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.