MolNFT v1 · #50238 · protein
Crystal structure of a protein with unknown function from DUF3225 family (ECA3500) from pectobacterium atrosepticum SCRI1043 at 2.32 a resolution
2RCD · Uncharacterized protein: “Crystal structure of a protein with unknown function from DUF3225 family (ECA3500) from pectobacterium…”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.71). MolNFT v1 #50238 on GenesisL1…
- PDB
- 2RCD
- Type
- protein
- Length
- 512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q6D1E8
- Ligands
- CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Uncharacterized protein | protein | 128 | 30% helix, 39% strand | Q6D1E8 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.71 | 0.76 | 92 | empty |
| 2 | 93 | 0.44 | 0.79 | 24 | empty |
| 3 | 92 | 0.41 | 0.78 | 25 | empty |
| 4 | 54 | 0.39 | 0.81 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1787 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 333 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 305 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 2RCD · Crystal structure of a protein with unknown function from DUF3225 family (ECA3500) from… · 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 Q6D1E8
- Elsewhere: RCSB PDB 2RCD · PDBe 2RCD · UniProt Q6D1E8
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