Research workbench
Crystal structure of a cupin protein (TM1459, H52A mutant) in copper (cu) substituted form
Analyse Crystal structure of a cupin protein (TM1459, H52A mutant) in copper (cu)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L2E
- Type
- protein
- Length
- 234 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CUPIN_2 domain-containing protein
- UniProt
- Q9X1H0
- Ligands
- CU
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CUPIN_2 domain-containing protein | protein | 118 | 5% helix, 61% strand | Q9X1H0 |
| B | CUPIN_2 domain-containing protein | protein | 116 | 5% helix, 60% strand | Q9X1H0 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains 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 | 157 | 0.50 | 0.78 | 22 | empty |
| 2 | 118 | 0.46 | 0.78 | 21 | empty |
| 3 | 127 | 0.44 | 0.77 | 24 | MES |
Interfaces
1 interface between chains.
- A–B · 1992 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6L2E · Crystal structure of a cupin protein (tm1459, H52A mutant) in copper (Cu) substituted form · 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 Q9X1H0
- Elsewhere: RCSB PDB 6L2E · PDBe 6L2E · UniProt Q9X1H0
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