Research workbench
Crystal structure of a cupin-2 domain containing protein (SFRI_3543) from shewanella frigidimarina ncimb 400 at 2.05 a resolution
Analyse Crystal structure of a cupin-2 domain containing protein (SFRI_3543) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D82
- Type
- protein
- Length
- 508 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cupin 2, conserved barrel domain protein
- UniProt
- Q07X94
- Ligands
- UNL, NI
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Cupin 2, conserved barrel domain protein | protein | 102 | 10% helix, 55% strand | Q07X94 |
| B, C | Cupin 2, conserved barrel domain protein | protein | 101 | 6% helix, 57% strand | Q07X94 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 5 copies · chains A, B, C, D, E
- NI · Nickel (II) ion · metal · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.79 | 0.82 | 53 | UNL, NI |
| 2 | 846 | 0.79 | 0.81 | 51 | UNL |
| 3 | 131 | 0.47 | 0.78 | 25 | empty |
| 4 | 128 | 0.45 | 0.77 | 21 | GOL |
| 5 | 64 | 0.44 | 0.81 | 17 | UNL |
Interfaces
4 interfaces between chains.
- D–E · 1508 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1207 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 672 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 599 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 3D82 · Crystal structure of a cupin-2 domain containing protein (sfri_3543) from shewanella… · 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 Q07X94
- Elsewhere: RCSB PDB 3D82 · PDBe 3D82 · UniProt Q07X94
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